Well an update as of the last few days, I have still not figured it out but have tried a few more things.

Smoke tested the intake manifold, unable to produce any results since eventually the smoke comes out the oil cap and the pcv hose and ends up everywhere but in the few seconds before it did that nothing was comeing from where it shouldn't. Pulled injectors out again and checked the spray pattern of this set and they look very nice, while they were out I stuck the boroscope down the ports again and could not see anything obstructing the spray pattern. Hooked the car up to the DRBIII yesterday and found out just what the PCM is thinking, Which is nothing short of logical, 190 - 202 degree coolant temps, 80 degree intake temps and the MAP is within 1 in hg of the mechanical boost gauge that I put in it to monitor, O2 sensor is bouncing around which is good and the fuel trims are not far out of whack at all which I was very surpised and kind of dissapointed to see, I would have thought that it was running lean since I do not smell any fuel when it starts missing. I put a fuel pressure gauge on and ducktaped it to the windshield for the drive home, It is not fluid filled so it jitters some but never went below 50psi and sat around 55 mostly. So the computer is not finding anything wrong with its inputs and the fuel pressure is not dropping out when it starts missing which I was hoping to see. That leads me back to the outputs, which means tearing into the harness since the coil, wires, and injectors are all from a running car.