My 97 FZJ80 started exhibiting those symptoms after the first 2+ miles of driving (heat-related). Come to a stop, hit the gas and the truck would shudder. Put it in neutral, hit the gas, no shudder. At speed, hit the gas, slight shudder. Oh cr*p, it has to be transmission related.
Nope: as mentioned in some other posts, part of the wiring harness runs close the EGR or too close to the EGR. Results: wiring, under acceleration, was rubbing and shorting out. It finally threw a cylinder misfire check engine light.
Here are the things I ruled out:
Plugs and wires: replaced
Head Gasket: checked for coolant leak / bubbles
Transmission: flushed fluid (almost made up my mind it was solenoid related)
Fuel Filter/Bad Gas: bought filter but finally had enough and took it to dealer ($140 fix)
Hope this helps.
Troy