However, my million dollar question for the group is whether a generic tune is good enough for our cars and if so, whether anyone had their tune screwed up after a reflash.
Bruce, my answer is that a competent source like Kenne Bell, Accufab, Ida, Muscle Motors, etc COULD (if they so desired) provide a generic tune for a STOCK car. This tune could provide performance benefits, change idling characteristics, fan speed turn-on points, etc. and could be applicable to just about anyone with a STOCK GT. They could do this and have good, consistent results and happy users.
HOWEVER, all bets are off when you start talkiing about individually modified cars.... then I think one size does not fit all. I believe your car has the Kenne Bell pulley/snout upgrade, Accufab throttle body, stiffener, and exhaust. This configuration would need to be individually tuned on your car by one of the competent sources above. (Let's assume it was.)
The tuner has the right to keep the parameters of that tune and if I call up one day and I have the exact same mods as you, the tuner could sell me the tune by installing into my SCT programmer and having me install it in my car. Odds are that the tune would work fine - but there is more risk that add'l tweaking may be necessary. Also, if there were differences such as I was running more or less boost than you (different pulley), then the changes would not work.... and my car should be tuned individually.
As you might imagine, these tuners build up quite a library of tunes that they can use as starting points. So, if I brought my car to John and I had everything the same as you but more boost, it would make sense that he download the tune he did for you and then start from there to tweak my car. I'm sure he would keep a copy of my tune and maybe this would be the starting point for someone else...
Regarding a re-flash.... this is a pretty generic term. The "tunes" downloaded into the ECU are in non-volatile memory and won't normally be effected by battery disconnects, etc. Another meaning of re-flash is that perhaps you take out your SCT programmer and attempt to re-install a tune previously developed for your car. A couple of things could go wrong. First, the SCT programmer will hold three unique tunes. The user could inadvertently download the wrong program. The second risk is that the tune on your programmer may not be reflective of the tune in your car.... due to an oversight by the original tuner.
In your case, I don't think the original tune was ever quite right and there were a couple of driveability problems. ANY competent tuner can correct the tune. I can't conceive of any advantage that the "the original tuner" has over any other tuner.... As I mentioned in my first post, there may be an economic advantage to go back to John as MAYBE he wouldn't charge you for the re-tune. Another tuner may charge you.... but there is no disadvantage or impairment that the new shop would have because you car was tuned somewhere else first. Most likely the new shop is going to start with their closest library match to your config and tune from there anyway.
FWIW, I purchased the SCT tuning software from SCT and now have the programming capability - but only for my own car by legal agreement. I have used/programmed engine management software before but the granularity of control provided by the SCT is simply amazing. This is a huge advantage to owning a GT over a car like the Gallardo or similar. (The GT has no peers!)