Chasing a miss and stumble

I too, am chasing a similar problem with my 1994 Trans Am. I am at the end of my rope on this one! I'm no dummy in the garage, as I've been a mechanic on a professional level for the last 16 years. But this problem has really called my bluff! Ok here is what I have, and what I am dealing with:
A 1994 Pontiac Trans Am with a brand new rebuilt LT1. The motor has been bored .030 over, Mahle forged pistons, Callies H-beam rods, stock crank reconditioned. Cam: Comp cams 07-501-8 cam, .488 .495 lift cam. I also replaced the roller lifters with new comp rollers as well. Stock 7.200 long pushrods, and the factory stamped steel rocker arms. The deck has been milled, as well as the heads, can't remember how much was taken off. The whole rotating assembly has been balanced as well. I am running a Lunati timing chain and gear set as well. The intake is stock, as well as the throttle body, injectors, and exhaust manifolds. I replaced the O2 sensors with brand new Bosch sensors, as well as the opti-spark with a reman Cardone distributor from Auto Zone. I run Autolite plug wires with TR-55 spark plugs. The computer has not been tuned as of yet. Now here is thr problem I am chasing:
I have a stumble, and or a miss in this engine that I absolutely cannot figure out. The old engine that was in this car had the same problem as well. It ran when I pulled it. I assumed the factory optispark was bad, or at least on its way out. Naturally I went out and bought a new one for my brand new engine. This did not cure the problem. I thought, ok..I have a faulty distributor. I tore the reman back off the engine and returned it to auto zone for a different one. Nothing changed. I replaced the ICM, and ignition coil with no change as well. The engine is underpowered at low RPM's with a bad stumble and miss, especially when accelerated lightly at cruising speed when the torque converter is locked up. When I give it WOT, it will stumble badly before it downshifts, then 6,500 rpms later it runs fine like it should. I checked for a bad plug, bad plug wire, and I have found nothing. I don't have any check engine lights on either. Now what could cause two engines to do this very same thing? I have over $6,000 invested in this new motor, and I don't want to blow it to the moon because of something stupid thats going wrong with it. PLEASE HELP!