Following all the wonderful advice from the people on the various forums I've been tracking down issues. First among these was the fact that I was only running on 2 cylinders as you can imagine this has a pretty dramatic effect on engine performance. It turns out this wire here was pretty important.
It provides the 12v to the 1st and 3rd cylinder injector. I got that tied into a 12v switched source to good success but the car still wouldnt really idle properly.
So I started on the big things that seems to always be mentioned. Vacuum leaks, igniter, TPS, IAC.
First I replaced the coil and igniter the one that was on the car was the original and not the set that came with the replacement engine. After the replacement the car wouldn't run at all. So I figured I just took a step backwards. I put the original back in and the car would barely run worse than before. I messed around with it and eventually got spark back.
After some reading I found that the igniter/coil ground on the mounts so I took it off again and wire brushed the mounting points and the bracket holding everything together. Put it back in and got a much better spark.
Last night I was looking thru the pbase pics of the MR2 and stumbled across the cut away of the intake manifold. It was here that I realized I had the mother of all vacuum leaks. The brake booster line was covered by the wiring harness and I had missed hooking it up.
Getting that sorted made the idle much better it explains why I had to basically floor it before to get it to even start. That's quite a lot of air going in that wasn't accounted for. The car will now settle down and idle on its own. Its not graceful but it's an improvement.
With the engine now idling on its own I can start bleeding the system. This will help the idle air control do its job better. It seems to be having an affect and idle is improving. This is the first time the car has been pumping water and I developed a leak at the thermostat. I replaced the clamp with one from the original engine and that cleared that up.
I was going to swap Throttle Position Sensors between engines to test that but I found the sensor on the original engine is designed 90 degrees out from the one on the current motor. So I broke out my multimeter and adjusted the one on the car.
Every change I've done has had a small improvement it not done but its getting there. Everything I've learned to look for I've found from threads on MR2OC and MR2.com. Thank you to the gurus that post there, the knowledge you've imparted has helped me a bunch. Here's where I'm currently at:
https://www.youtube.com/watch?v=5Wu46Zl6O00