FSJ vacuum routing can be daunting to look at. Here's a quick rundown on routing for a mid-80's FSJ. Different model years used slightly different vacuum routing. See links at the bottom for a great site on vac diagrams for various model years. For definitions of the devices and what they do, check this article on vacuum emissions systems.
Here's a large, hi res diagram that is color coded to make it a little easier to distinguish between different vacuum sources. We'll dissect this thing piece by piece to make it easier to figure out.

There are a few minor differences between 85 and 86+ so here is an underhood vac diagram for 88 to reference for some stuff. Big thanks to Tom 'Oljeep' Collins for putting all these diagrams (and more) in one place!
88_FSJ_Vacuum_360.jpg
Let's step thru it...
Start with the distributor vac advance... this traces back to the middle output of the HDC CTO; that's the CTO on the thermostat housing. The middle of these type of CTO's is the "output" so to speak. Based on temp, it selects from one of two "inputs".

This particular CTO draws signal from one of two sources: the Spark CTO when the engine is warm, or manifold vacuum if the engine is TOO HOT. Why? Because the theory is that this will bump up the idle and thus cool the engine down. Does this work? Absolutely not! But hey, it sounds good, right? This CTO plugs into a whole gang of manifold vacuum tubing that is connected to the carburetor (center, for the power valve), and a brass fitting on the front manifold.

Tracing the other HDC CTO signal, it goes back to the center "output" of the Spark CTO above. The Spark CTO decides whether the vacuum advance gets manifold (cold) or ported vacuum (warm). On the warm side, ported vacuum traces back to the passenger side of the carb. It does branch off to that mysterious device (NLVR), but ignore that for the moment. Ported vacuum also traces to the purge valve on the emissions canister (not highlighted here; refer to the complete spark diagram later on). So when the engine is warm it gets ported vacuum.

The other "input" traces to the Non-Linear Vacuum Regulator, above -- this is a fancy device that simply limits the amount of vacuum signal going to the vacuum advance. All it really does is takes manifold and ported vacuum and regulates between the two to get the right signal. The output is at the top in the diagram. The manifold vacuum input is in the middle, and hooks into that same brass fitting as above. The ported input hooks into the ported signal we just talked about.
(When you get multiple devices branching off the same source (like the ported vacuum source on the carb) the best way to think through it is that they act independently. They have no influence on each other. The carb is sending the same signal to each. Don't know if that helps)
Ok, so that takes care of the entire spark advance system. Here's everything put together, below. You have your cold operation: vacuum signal comes from NLVR mixing manifold & ported. Your too-hot operation: manifold vacuum. Your normal temp: operates off ported.

You can simply all this if you so choose. First, remove the NLVR. Where it "taps into" a vac line, replace the T with a straight adapter or run new line. What you end up with is the Spark CTO gets Manifold vacuum when cold, and ported when hot. This is how the earlier model FSJs were "wired". You can also ditch the high temp (HDC) CTO. Run the Vac advance line direct to the Spark CTO "output" (middle). Remove the T fitting for the HDC CTO that goes to manifold and replace with straight or run new line. Make sure you preserve a manifold vac signal going to the power valve!! (or else it will always be on!) This greatly simplifies the spaghetti. You now have one CTO where you used to have a 2 CTOs and an NLVR.
Let's move on to the the EGR system. Starting at the EGR itself, it gets a vacuum signal to turn it on. But we only want to turn it on if the air drawn into the motor is warm. To do that, there is a sensor on the side of the air cleaner housing called the TVS (Thermal Vacuum Switch). When it's warm, it lets vacuum through. When it's cold, it blocks vacuum signal, disabling the EGR.

Now, on my rig, there was a vacuum line that T'ed off the TVS to the purge signal. Anyway, trace back the signal from the other side of the TVS to ... yet another CTO! Actually... this one is a DUAL CTO -- two in one package. Whee. All it is doing is ensuring the EGR is enabled only if the engine coolant temp is warm. Thus, EGR only comes on when both engine coolant and intake are are warm. Simple. Tracing back from this CTO we arrive at the EGR port of the carburetor, the driver side port. Couldn't be easier right? Also, there's usually a delay valve inline between the EGR and the TVS. However, one service bulletin fix for pinging is to remove this. So you may not have it. That's the EGR system.
Let's look at the AIR system. There's an AIR Control Valve that on later model rigs uses two signals. One diverts air between the exhaust manifolds and the catalytic converter. The other turns the device on and off. You can reference the 88 diagram for this additional detail. Trace the signal back from the valve through a reverse delay (R/Delay) valve back to manifold vacuum--this is the signal that turns the device on when the engine is running.

The R/Delay holds the vacuum signal to the device so that during acceleration when the manifold signal drops, the valve stays open. The other signal traces all the way back to that Dual CTO we talked about, and down to a manifold vacuum signal. This controls whether the output of the AIR pump is sent to the manifold or catalytic converter, based on engine temp as well as engine load -- under acceleration the signal goes away which should divert air to the cat (to address the vehicle running rich). When cold or under cruise, the air is sent to the manifolds to further oxidize the outputs of combustion.
The Thermal Air Control (TAC) system operates the valves on your air cleaner snorkle using manifold vacuum. When the engine is on, manifold vacuum is held and applied to the main valve. A TAC sensor, in essence a thermal vacuum switch, tells the second valve to select hot air from over the exhaust manifold (the silvery corrugated downpipe that you probably lost years ago) or, once the engine is warm, from cooler outside air (the corrugated black tube going to the front of the engine bay near the battery if you didn't lose that too). See below for this basic system. The check valve holds vacuum on the main motor (evaporatie system motor) to keep the valve open at all times.

And that's pretty much it. You also have a giant vacuum tube going from the front manifold brass fitting to the brake booster, and there's supposed to be a vacuum signal going to the round ball -- a vacuum reservoir for your 4x4 and heater. And also vacuum to the black coffee can on the passenger side-- your cruise control reservoir. Those aren't shown on the diagram.

The diagram above shows your PCV routing, bowl vent routing, and gas tank vent routing.
Added 01/04/08
Thanks to Strider on IFSJA BBS for providing this graphic of a simplified spark advance. I did this on my rig some time ago for testing, and it seems to work fine. Basically you're eliminating the 2nd CTO and the NLVR. This really cleans up the spaghetti.

Now that you know everything about vacuum routing, take a peek at this article on vacuum emissions systems for detailed explanations of each of the devices.
The best collection of FSJ vacuum diagrams has to be Tom 'Oljeep' Collins' website, hands down. He also has great electrical schematics for various years and myriad other reference material.
Here's a large, hi res diagram that is color coded to make it a little easier to distinguish between different vacuum sources. We'll dissect this thing piece by piece to make it easier to figure out.
There are a few minor differences between 85 and 86+ so here is an underhood vac diagram for 88 to reference for some stuff. Big thanks to Tom 'Oljeep' Collins for putting all these diagrams (and more) in one place!
88_FSJ_Vacuum_360.jpg
Let's step thru it...
Spark Advance
Start with the distributor vac advance... this traces back to the middle output of the HDC CTO; that's the CTO on the thermostat housing. The middle of these type of CTO's is the "output" so to speak. Based on temp, it selects from one of two "inputs".

This particular CTO draws signal from one of two sources: the Spark CTO when the engine is warm, or manifold vacuum if the engine is TOO HOT. Why? Because the theory is that this will bump up the idle and thus cool the engine down. Does this work? Absolutely not! But hey, it sounds good, right? This CTO plugs into a whole gang of manifold vacuum tubing that is connected to the carburetor (center, for the power valve), and a brass fitting on the front manifold.

Tracing the other HDC CTO signal, it goes back to the center "output" of the Spark CTO above. The Spark CTO decides whether the vacuum advance gets manifold (cold) or ported vacuum (warm). On the warm side, ported vacuum traces back to the passenger side of the carb. It does branch off to that mysterious device (NLVR), but ignore that for the moment. Ported vacuum also traces to the purge valve on the emissions canister (not highlighted here; refer to the complete spark diagram later on). So when the engine is warm it gets ported vacuum.

The other "input" traces to the Non-Linear Vacuum Regulator, above -- this is a fancy device that simply limits the amount of vacuum signal going to the vacuum advance. All it really does is takes manifold and ported vacuum and regulates between the two to get the right signal. The output is at the top in the diagram. The manifold vacuum input is in the middle, and hooks into that same brass fitting as above. The ported input hooks into the ported signal we just talked about.
(When you get multiple devices branching off the same source (like the ported vacuum source on the carb) the best way to think through it is that they act independently. They have no influence on each other. The carb is sending the same signal to each. Don't know if that helps)
Ok, so that takes care of the entire spark advance system. Here's everything put together, below. You have your cold operation: vacuum signal comes from NLVR mixing manifold & ported. Your too-hot operation: manifold vacuum. Your normal temp: operates off ported.

You can simply all this if you so choose. First, remove the NLVR. Where it "taps into" a vac line, replace the T with a straight adapter or run new line. What you end up with is the Spark CTO gets Manifold vacuum when cold, and ported when hot. This is how the earlier model FSJs were "wired". You can also ditch the high temp (HDC) CTO. Run the Vac advance line direct to the Spark CTO "output" (middle). Remove the T fitting for the HDC CTO that goes to manifold and replace with straight or run new line. Make sure you preserve a manifold vac signal going to the power valve!! (or else it will always be on!) This greatly simplifies the spaghetti. You now have one CTO where you used to have a 2 CTOs and an NLVR.
EGR System
Let's move on to the the EGR system. Starting at the EGR itself, it gets a vacuum signal to turn it on. But we only want to turn it on if the air drawn into the motor is warm. To do that, there is a sensor on the side of the air cleaner housing called the TVS (Thermal Vacuum Switch). When it's warm, it lets vacuum through. When it's cold, it blocks vacuum signal, disabling the EGR.

Now, on my rig, there was a vacuum line that T'ed off the TVS to the purge signal. Anyway, trace back the signal from the other side of the TVS to ... yet another CTO! Actually... this one is a DUAL CTO -- two in one package. Whee. All it is doing is ensuring the EGR is enabled only if the engine coolant temp is warm. Thus, EGR only comes on when both engine coolant and intake are are warm. Simple. Tracing back from this CTO we arrive at the EGR port of the carburetor, the driver side port. Couldn't be easier right? Also, there's usually a delay valve inline between the EGR and the TVS. However, one service bulletin fix for pinging is to remove this. So you may not have it. That's the EGR system.
AIR System
Let's look at the AIR system. There's an AIR Control Valve that on later model rigs uses two signals. One diverts air between the exhaust manifolds and the catalytic converter. The other turns the device on and off. You can reference the 88 diagram for this additional detail. Trace the signal back from the valve through a reverse delay (R/Delay) valve back to manifold vacuum--this is the signal that turns the device on when the engine is running.

The R/Delay holds the vacuum signal to the device so that during acceleration when the manifold signal drops, the valve stays open. The other signal traces all the way back to that Dual CTO we talked about, and down to a manifold vacuum signal. This controls whether the output of the AIR pump is sent to the manifold or catalytic converter, based on engine temp as well as engine load -- under acceleration the signal goes away which should divert air to the cat (to address the vehicle running rich). When cold or under cruise, the air is sent to the manifolds to further oxidize the outputs of combustion.
Thermal Air Control
The Thermal Air Control (TAC) system operates the valves on your air cleaner snorkle using manifold vacuum. When the engine is on, manifold vacuum is held and applied to the main valve. A TAC sensor, in essence a thermal vacuum switch, tells the second valve to select hot air from over the exhaust manifold (the silvery corrugated downpipe that you probably lost years ago) or, once the engine is warm, from cooler outside air (the corrugated black tube going to the front of the engine bay near the battery if you didn't lose that too). See below for this basic system. The check valve holds vacuum on the main motor (evaporatie system motor) to keep the valve open at all times.

Odds and Ends
And that's pretty much it. You also have a giant vacuum tube going from the front manifold brass fitting to the brake booster, and there's supposed to be a vacuum signal going to the round ball -- a vacuum reservoir for your 4x4 and heater. And also vacuum to the black coffee can on the passenger side-- your cruise control reservoir. Those aren't shown on the diagram.

The diagram above shows your PCV routing, bowl vent routing, and gas tank vent routing.
Simplification
Added 01/04/08
Thanks to Strider on IFSJA BBS for providing this graphic of a simplified spark advance. I did this on my rig some time ago for testing, and it seems to work fine. Basically you're eliminating the 2nd CTO and the NLVR. This really cleans up the spaghetti.

Now that you know everything about vacuum routing, take a peek at this article on vacuum emissions systems for detailed explanations of each of the devices.
Links
The best collection of FSJ vacuum diagrams has to be Tom 'Oljeep' Collins' website, hands down. He also has great electrical schematics for various years and myriad other reference material.




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