Wow, me and the 'bird have come a long way since this post originally started. Here's some updates:
The manual fan control is installed(no big trouble, just time) with desired results. I never have changed the thermostat, but with the fan control I can keep the temp right there without waiting for the fans to automatically kick on 20+ degrees later. It still allows for the fans to operate normally during daily driving, so I see no disadvantages to it.
I've never run it without the filter at our dirty country boy dragstrip(actually the track is quite well cleaned and prepped, but surrounding areas are rough), but for whatever it is worth, on the dyno my car picked up over 10 hp & tq when I removed the filter.
Time learning my car and several more passes

down the strip have taught me the most important factor in getting the most out of my car at the drags are good launches. As for the "electronic" tuning, I've got plans for the Tech 2 scan tool and LS1 edit the next time I go, probably sooner rather than later. Just need to knock out some scheduled fluid changes before then to make sure everything is in tip-top shape. You know, take care of your 'bird and she'll take care of you sort of things...
I'll let you guys know how it goes.