I just finshed reading about a dozen posts on cylinder misfires, still puzzled.
2000 3.4, 189000 mi. Starts and runs fine when cold, meaning first start in the morning. I can drive about 20 miles and it runs well. If I shut it off and restart, it starts a slight miss which gets worse while driving and after about 10 minutes will turn on the check eng. light. Starting it anytime without waiting for a complete cool down (overnight) it will still miss.
I put the code reader on it pulled P0171, P0300, p0303, p0306. So cyl. 3 & 6 are misfiring. I changed the coil on 3 and replaced all plugs, wires and coil boots. NGK wires, boots and Denso plugs. Also cleaned MAF while it was apart. Fired up and ran like new! Drove around for about 45 minutes, no problems. Ran a lot better than before, looked like the original plugs and wires in it. All plugs were worn badly but #3 was by far the worst. Anyway, next day started up to run errands, drove about 15 miles, stopped, came out and started it up, SOS! Same codes, same everything!
Lean mixture on 3 and 6, cyl misfires on 3 and 6. Am I right on thinking this is ignition related or could it be injectors on those two cyl. failing at the same time?

Could be dirty injectors, faulty MAF, faulty ignition module. Considering the things you DID change.

I noticed you mentioned "hot engine misfire" in the title. I had something similar happen to me in my 4R. I got p0171, p0300, and some others. In my case, I would drive my truck for 20 min or more. Its all warmed up and the truck would shut off while driving and start back up on its own (quite violent). Now that's different then your case, but it only happened while the engine was hot. I diagnosed for weeks and changed many parts related to the codes. Found the problem - A Bad Ground on the intake manifold. Something so small was causing these crazy symptoms. Check all your grounds in the engine bay. The ignition wires are grounded on the intake manifold for my 2001 SR5.

FSM Diagnostics of all of those codes being thrown, then removed by new parts or whatever, then returning, all points to the ECM going south.... or what FLORUNNER said......my .02

Where did you get your replacement parts from? Reason I ask is because I put in some new Denso plugs from ebay in and my 4runner would start missing a lot after warm. I believe the plugs I bought were fake Denso's.

Thanks for the feedback. You know I'll be out there checking grounds tomorrow!
About the parts, I was a arts guy for 23 years, retired from NAPA in 2012. I know what I'm buying!
Thanks again guys for replies!

You can also try swapping coils around to see if it follows.

-Charlie

You're most likely getting misfires on those to cylinders due to then running lean I'd check the resistance on injectors cylinder 6 might get hard to reach with out taking the intake off. Resistance should be 13.8 ohms at about 70 degrees. You can also try to listen to them with long screw driver they should click nice and crisp.

wallyk50, did you ever get that issue sorted? I have a '99 3.4 with 330k doing the same thing, just cyl's 1&4 instead of 3&6. I did the exact same thing you did -- replaced the shared coil, plugs and wires... SOS. I'm leaning ignitor, injectors, or ECM, in that order... Thanks!

Getting an 0171 also?

No, no 0171. Just the 0301, 0304 [misfire Cyl's 1 & 4], and 0300 [multiple misfires detected]. I took it in to a local shop to put on their diagnostic machine. Hopefully they can point me in the right direction.

Local shop had it for over a week. They're stumped and giving up, and I'm picking back up today. I'm going to throw a used but known-working igniter at it and see what happens.

If anyone has a flash of brilliance, I could use the illumination about now... Thx!

NOT the igniter. The search continues.

You might know about the best features of your car, but not about the important car parts. It is important to have detailed knowledge about your buy engine parts so that whenever you meet an uncertainty, you can explain the problem well to the mechanic and get it resolved quickly.