Ongoing issues with CEL 25, 25/26 on 94 fzj80 (1 Viewer)

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I'll separate this thread into two sections as the issues may or may not be related.

For a few months, I had been dealing with CEL 25 and 26 (Lean/Rich), overall sluggish performance, rough idle, exhaust smelled rich even after warm-up, and poor fuel economy.
Things I did:
- Replace O2 sensors and cleaned connections - Had no effect
- Examine spark plugs
- Checked intake tube for cracks
- Checked around intake for leaks
- Checked exhaust pre-O2 sensor for leaks
- Bench tested VAF - met FSM specs
- Checked overall for apparent vacuum leaks
- EGR was recently replaced by the previous owner less than 10k ago.
- PAIR afaik is original
- Wiring harness under the EGR has some heat wrap around it from the PO, so at some point someone was in there either fixing it, or preventing it from melting.

I took it to a toyota shop to have them inspect, they believed the issue lied between the VAF, engine harness, and ECU with the ECU ultimately getting an invalid IAT reading as it was running extremely rich. They said the next step would be to do a pinout but that labor hours would likely be costly so I declined and decided to pursue on my own with this new information.
The next step I took was to replace the PCV lines as one had an obvious crack and just for good measure I disconnected the VAF, sprayed the connectors with a little electrical cleaner and voila! CELs went away and she drove better than she ever has. Can I say for certain that's what actually fixed it? No. But for the next 400 miles (roughly 3 weeks) it ran perfectly, city, highway, high altitude wheeling on a very bumpy rocky road, it seemed like my problem was gone. During this time I also started working on replacing vacuum lines (ewg, fpr, vcv) as part of PM and replaced the charcoal filter and evap lines. No issues afterwards.


Fast forward to this weekend, as I'm preparing the rig to ultimately have a fridge, I installed @landtank high output alternator. The install goes well, no issues, and I turn her on and I immediately notice a rough, low idle, and overall loss of power. I drive it around a little bit thinking maybe its just because I reset the ECU, but within a mile I have CEL 25.

My first thought is that I must have bumped or forgotten to reconnect something while I was in the engine bay working. It was working perfectly before, and now it is not. So I'm assuming this is a new issue, but maybe its the same issue as before just triggered by an ECU reset or random happenstance? I'm not noticing anything apparent in the engine bay where I was working.
- Charcoal cannister lines are connected and in good shape
- FPR lines are still connected
- VCV lines weren't touched
- all the grounds are firmly connected
- battery terminal is clean and tight
- distributor spark plug wires and coil wire are seated and seem in good shape (though the lines say 2011 so I'll replace those just in case)
- No obvious disconnected vacuum lines, or electrical connections
- Alternator is charging appropriately
- Nothing changes the low rough idle when wiggled and I tried to wiggle everything in the area of the alternator, also tried spraying any vaccuum lines in the area with carb cleaner
I did have to put tension on the wire harness to the alternator as the upgraded alternator seems to be clocked farther than OEM. Is it possible one of those wires broke? Would that cause a lean condition?

At this point I'm not sure where to look next. Do I continue diagnosing as if this is still the original problem and expand to fuel system, engine harness under the EGR, possibly bad ECM, PAIR, FPR, etc, or look specifically for things around the alternator which at this point seem to point to damage to the wiring harness?
 
Agree with @BTLSHP - best to confirm the systems listed in FSM one by one are to spec.

Only thing I would offer additionally based on my experience: The VAF FSM check is very basic. It just confirms that the temp sensor gives reasonable values, and that the VAF flow mechanism isn't completely obviously broken. It however it doesn't at all ascertain that the VAF flow output is correct in any way. Not saying the VAF is the issue, but I wouldn't discard as the cause purely based on the FSM check.
 
One more thing: If you don't have it already, I think it's worth getting a bluetooth OBD 1 reader like this here: OBD1READ with Bare wires - https://zf-scantools.com/index.php?rt=product/product&path=71&product_id=126

You can connect an Android app to it and conveniently see the main parameters the ECU is monitoring. It has a few quirks, e.g. at least for me the lean/rich indicator is inverted. But I found it extremely helpful in observing rough running engine issues and get a feel for the behaviour around it. Together with some understanding of the overall system and common sense, it may allow you to prioritize the FSM list or rule out certain things.

E.g. in your case, is it always lean? If only sometimes, under which conditions (hot, cold, partial load, low load, high load)? Do the other values look reasonable? ECT temp reasonable? VAF value? For mine, it is around 2.7V at warm idle in P/N and A/C off. 0.5V is wide open throttle near max power, however this maybe lower if you're at sea level, maybe 0.4V.
Screenshot_20250509-223043.jpg
 
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One more thing: If you don't have it already, I think it's worth getting a bluetooth OBD 1 reader like this here: OBD1READ with Bare wires - https://zf-scantools.com/index.php?rt=product/product&path=71&product_id=126

You can connect an Android app to it and conveniently see the main parameters the ECU is monitoring. It has a few quirks, e.g. at least for me the lean/rich indicator is inverted. But I found it extremely helpful in observing rough running engine issues and get a feel for the behaviour around it. Together with some understanding of the overall system and common sense, it may allow you to prioritize the FSM list or rule out certain things.

E.g. in your case, is it always lean? If only sometimes, under which conditions (hot, cold, partial load, low load, high load)? Do the other values look reasonable? ECT temp reasonable? VAF value? For mine, it is around 2.7V at warm idle in P/N and A/C off. 0.5V is wide open throttle near max power, however this maybe lower if you're at sea level, maybe 0.4V.
View attachment 3917600
Ah, now I know what the VAF field is referring to on mine! Light dawns on marble head.
 
I would start with the assumption that these new symptoms are unrelated, and the last things you touched (alternator install, vacuum lines, FPR, Vacuum VSV, etc.) caused the new issue. 99% of the time for me, it is something there - I failed to reconnect something, connected something wrong, bumped another part, broke something inadvertently, etc. If you can't find what you did to cause it after some reasonable amount of time, work your way through the full FSM troubleshooting guide without making any assumptions or skipping steps. This is very time consuming to do properly, and if you are anything like me, you will find yourself tempted to make assumptions and skip steps. Fight that urge as much as possible.

As an aside, what is ewg?

You said "replacing vacuum lines (ewg, fpr, vcv)"
 
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I had same set of CEL errors until I cleaned out the goo in the throttle body / manifold passages and got the correct set of O2 sensors in my 94. Then all went away.
 

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