Also would you care to share what your old fashioned scientific process found? I have my suspicions, but I rather hear it from the horse's mouth. It would most likely be of great benefit to others running the same TT system.
I will start a new thread in a bit with the intent of sharing some insight. I'm not so sure astute people like you will get much from it as I think you've probably kept pretty good track of the path we've been on. We did, with the help of Jason and others, improve on a few components that, in retrospect probably wouldn't surprise anyone.
We also had a couple of opportunities to laugh at ourselves. Several days before the last (successful) dyno day you may recall that we had the car on the dyno and experienced fuel pressure anomolies that prevented us from doing any tuning North of 20psi. Many potential failure points were going through my mind (bad fuel pumps, clogged filters, bad relays, etc.) and we brought the car back home to begin diagnosis. Fortunately, it didn't take us long to pinpoint that it was OUR work that led to the problem. It was as simple as a bad ground at the BAP. A very fast and easy fix and a proof point that as careful and methodical as you try to be, errors can still be made!!