98 V6 Wont rev over 3500 - Detailed

It could quite literally be a Torque Convertor. But I would expect the 4Runner ECU/TCU to be a bit smarter than that and fire off a Input/Output shaft correlation to RPM error.
 
First off I'm blown away with your determination, you've been after this problem for a long time. I looked through the tread a couple times to see if you did the TPS and other than mentioning it early on I didn't see anything else about it. FWIW I had a very similar sounding problem (I did lock a code but it was intermittent so I figure the computer must need to see something pretty messed up with the TPS signal before it locks the code which means you could have a failing sensor that isn't bad enough to lock a code but could still effect drive-ability) and it was the TPS. I tried to troubleshoot it w/a DVOM (I know you should use an analog meter but it's what I had) and didn't see anything off. It was a cheap part so I swapped it and the change was instantaneous. There wasn't any change in power below 3500, but it didn't cut out anymore. If you did R2 it and I missed it, sorry for the needless post and I hope you get it run down.
 
First off I'm blown away with your determination, you've been after this problem for a long time. I looked through the tread a couple times to see if you did the TPS and other than mentioning it early on I didn't see anything else about it. FWIW I had a very similar sounding problem (I did lock a code but it was intermittent so I figure the computer must need to see something pretty messed up with the TPS signal before it locks the code which means you could have a failing sensor that isn't bad enough to lock a code but could still effect drive-ability) and it was the TPS. I tried to troubleshoot it w/a DVOM (I know you should use an analog meter but it's what I had) and didn't see anything off. It was a cheap part so I swapped it and the change was instantaneous. There wasn't any change in power below 3500, but it didn't cut out anymore. If you did R2 it and I missed it, sorry for the needless post and I hope you get it run down.

We tested the TPS but never replaced it. Tests 'appear' normal with a meter and with live data showing constant throttle position movement from 0% up.
We should maybe consider replacing it, I'll check it out.
 
Unless you have the ability to keep buying parts for some time, I'd at least get a scanner that reads live data. See if something goes amiss at 3500 rpms and higher.
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At 3500 it starts misfiring, but my opinion was this was a side effect of what was causing the problem.
Since everything in the ignition had already been replaced, we went with the heads and had them rebuilt.
The tech that did the live data suggested the non oem coil packs could cause this, but I find it hard to believe that the problem wouldnt have at least changed a bit and not stayed EXACTLY the same with the replacement parts.
 
In regards to the Alternator -

We simply removed the belt and cranked the truck and problem remained.
I cant imagine that we have to actually replace the alt to test if its the problem??
 

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