If I were in your shoes, I'd re-post this thread over on LS1Tech.
For what it's worth, it's next to impossible to diagnose ecu/injection issues over the web. I had similar issues with my GM electronics this past spring. I had the owner/tuner of Vengeance Racing in my shop with the absolute latest and greatest tuning equipment and software, and he shrugged his shoulders after an hour and left. I bought a a Mast M90 setup, and all is well.
It was probably something simple in my case, I just ran out of time.
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