I am starting on my 3.4 swap into a 94 5speed 4runner and found a donor engine with the wiring harness and ecu from an 01 automatic 4runner. My question is about the Drive by wire stuff. I plan on doing my own wiring and was wondering if connecting resistors to satisfy the automatic ECU will still work even though its the drive by wire. Is there another option, like finding a manual ecu from a tacoma or does drive by wire mess that up.

I read a lot of ECU discussions when doing my swap. I recall people bypassing the neutral circuit on the auto ECUs for use in a M/T. I didn't have the desire to spend time on that so I found a M/T ECU, but they are much harder to find. As far as drive by wire, the 5VZ throttle bodies are pretty easy to find. You could swap to a cable operated body very easily.