Kyle, you've seen my modified Trojan (blue grip guy). I am having another made for me by RK. I selected 40 again. I load the system mags by Tripp, and have a soft minor load. IF, so inclined by a stage preview before I declare my power factor, I find that the stages and reloads do not warrant 10 round, I could load major. I haven't been doing so, but I like the flexibility.
My wife just moved from her Tanfo standard pistol into an STI USPSA in 9mm. She runs Tripp mags as well (the need tuning but once done, are very reliable). She loves the pistol, and after a trigger job will be perfect. 9mm through the 1911 frame is much different than mine. While my minor set up feels soft and VERY flat, her's (at 129pf N320 rounds) is a little snappier, but very quick feeling (and she prefers that feel, coming from a Standard major pf).
I don't think you can go wrong with either calibre, its basically a matter of your preference and what you may be set up to use (and although I love 45ACP, I am not included to use for high volume competitions....).
Oh, and I can fit the box with my 5" STI and that is with a larger Techwell magwell. The mags are trimmed at the factory to fit. It is a tight fit, but a fit nevertheless.