Hi All,

Been lurking these forums since I bought my 4Runner in January. I've come across some misfire issues and have yet to find a remedy.

The vehicle is a 2000 4R Limited with 4WD and Rear Locker.

On initial cold start, it runs great, no issues whatsoever, no codes, no lights, no indication of any problem.
The problem however arises when I drive it and park it for let's say 20-30 mins. I would start it again and would get shaking after about a minute. When this happens, it seems to go into limp mode and I cannot go past 1500rpm. Sometimes I'll get a code (P0300, P0301, P0303, P0305, P0306). Most times, it'll just show a pending code. If I give it a couple revs, it'll usually fix it and it'll drive just fine again or if I turn it off and start it back up, it's fine. If I drive it and park it overnight and start it again, I have zero issues. Seems to happen only after it sits for 30-45 min and I drive it again.

Here is all that I have replaced with new OEM Toyota parts: TPS, MAF, spark plugs, crank position sensor, and air filter.
My mechanic, as well as another friend who ran into a similar issue, but only on cold start told me that it may be early signs of a failing head gasket. Sounded like coolant may have been seeping into the cylinder and causing the shaking until the excess coolant was burned off. At this point, I had run out of options. I went ahead and did the head gasket as well as other misc things that needed to get done anyways. Head gasket work was done along with a new knock sensor harness since mine was old and brittle, spark plug wires, coil packs (only OEM Denso).

However...$3k later with all these new parts, machining the heads, reseating the valves with new seals, new OEM injectors, and a new fuel filter...I'm still running into the same misfiring issues. It's also worth noting that the engine was replaced at some point as the VIN plate was from a different 4runner.
Any ideas what it could be? There was an issue with the throttle body sticking. If the throttle body is forced closed, the motor will begin to shake like it's misfiring. I also don't know if the fuel pump was ever changed, so I'm not sure if maybe the motor is bogging from a failing pump not supplying enough fuel to the injectors. The other concern was that because of how old the car is, the harness for the fuel injectors may be brittle so we may need to finagle with it. Aside from those 3 things...I am completely lost. Any help would be greatly appreciated.