Finally had a chance to look over 1-5.dat
Some observations (for what they're worth):
Tranny doesn't look to bad, EXCEPT, what I did see was your TCC is locking simultaneously with the 2-3 shift

Notice the engine rpm dropped over 1,600, all the way down to 3,300. Pretty bad bogg because of it too. If you're not locking it at that point, something else is. Probably why the 2-3 shift felt so "luggy".
Never did shift into 4th, or didn't indicate such.
Driving those injectors to 150%

I think you'll find that 42.5's might be close to 100% by the time you get them in. You may have to go larger. I'd seriously re-think your next injector upgrade!
Judging from the fact that the chip is running 27.4º of WOT spark timing, it's likely a 108 chip. Most 100 chips are closer to the 23-25º range. You have too much timing for a 100 chip.
As for the voltage that was mentioned. It's really NOT too low. Anybody runs DS will probably notice the voltage "seems" to be lower than it should be, but that's more a function of DS than it is voltage, simply because of where it's "tapped" and read inside the ECM. I wouldn't worry too much about that. A perfectly normal operating system will usually indicate voltages in the 12.4-13 range on DS during WOT.
Other than that, not much else. Just don't lock the TCC until after you've been in 3rd for at least 2 seconds, then you won't have that HUGE 2-3 bogg.