Finally figured out the problem in H8pvmnts old 3RZ. Between my work and the shops, we tried alot of things. The shop is a mostly toyota shop and the mechanic has done over 10 3.4 swaps and 4 3rz swaps. He works on these every day, and we still had to just keep trying things, because even his new Snap on scanner didn't really help.
In the end, after checking wiring, changing O2 sensors, TPS, CPS checking valves, vacum lines, ecu, etc....
IT WAS THE FUEL INJECTORS.
The strange thing was that they were all apparently bad. All the plugs were fouled out.
We changed the whole fuel rail, regulator, and injectors together from a parts engine. The computer was trying to richen things up, and it smelled rich because of exhuast leaks and strange injector behavior, but it was just running out of fuel. When we misted fuel into the intake while reving it, it reved up quickly and much better. So we tried the injectors.
Even pinching off the return line didn't fix it so we figured it wasn't fuel pressure to the rail.
Anyways, it still surges a little here and there, but it still has exaust leaks and has an older reman MAF. Its obvious the main problem is fixed though. Hope this helps some others. Heading to the oregon dunes with this and a rzr 900 next weekend...
Thanks everyone.