So a couple weeks ago my wife's 1999 4runner (3.4) 148k miles started shuddering acting like it was missing. Finally threw a code a few minutes after stating a mis-fire on cylinder #6. It would only act up if it was drove, got hot, stopped for 5 minutes and started again. This ended up being an intermittent issue with the #6 injector.

Initially I changed spark plugs to the NGK dual electrode ones since that was the quick but that didn't do anything.

Ended up swapping the #6 injector from another 3.4 engine I have. The bad miss went away but I noticed if you jabbed thr throttle either on the throttle body or gas pedal while it's idling, there was a 1-2 second hesitant/bog.

Put all new OEM injectors in, no change but it runs a lot better overall

Put new plug wires in, no change

Changed fuel filter with new OEM one, no change.

Cleaned MAF, no change

If you accelerate moderate to slow you'd never know. Id drives fine other than this issue and it only happens when you pretty much floor it from an idle even while it's in neutral just sitting.

I'm about out of ideas other than clean the throttle body... Any help would be greatly appreciated.

 

You didn't mention bank 1 o2 sensor. Now is the time to invest in a bluetooth or wifi odb2 plug and get the torque app on your phone. Monitor the live data and see if your bank 1 o2 is cycling up and down properly, monitor coolant temps, read you MAF sensor and see if it's flowing the right amount of air, monitor your timing advance. I've had a misfire turn out to the a bad crank sensor but there's proper ohm specs for it in the FSM, same for camshaft sensor. Usually misfires like that are simply plugs and wires, but if you've changed them, then rule that out. The coils are really really durable, but you could swap them around. Check really good for vacuum leaks. Also your new odb2 dongle will let you view your short term fuel trims and long term. If you long term trims are off, could indicate a vacuum leak, or air getting in after the MAF. Stock intake? Hmm just brainstorming- good luck.