which ecu did you use?  did you leave all the wire harness that is attached to the 93 motor or did you reuse the harness from the 90 motor, because i have put a 92 v6 truck motor in a 1988  truck, but never fool with a 4 runner, when i did this swap, i took every thing that was in the 92 truck including all the vacum crap and the ecu and it works fine, it be kinda hard to mix 90 stuff to a 93 motor