Gotcha, so it's intermittent. Stan is right in that because this EFI system is pre OBD2 we don't have the diagnostic or telemetry advantages of OBD2, so it's more difficult to figure out which sensor is malfunctioning.
I find it really hard to believe that there are no codes, especially because you completely removed the EGR. At very least there should be an EGR code.
Can you drive it for maybe 50 miles and let us know if the CEL comes on or if the driveability changes?
On the OBDI trucks it won't throw a code. The OBDII trucks require a resistor to fool the EGR temp gauge so it won't throw a code.
At least that is my understanding of the 1FZ desmog when I looked in to it a few years back.
While this is most likely not the actual problem a friend of mine did have a trooper that was having slightly similar problems and after months and months it turned out the ECU had become damaged somehow and intermittently having issues. Sounds strange as to me a ECU going bad would be bad all the time or at least all the time after it warmed up and got hot. But a ECU from the junkyard fixed it right up. I wouldn't recommend chasing that rabbit now though as i'm sure with the help of the knowledge from Johnny and the rest of the club it the answer will be found.