If you want a new TMIC I'd install it pre tune so that it can adjust itself into the tune with the rest of the new stuff. Otherwise it will have to go through a whole new learning process(driving easy/mild for 20+ miles). The Cobb AP's stage 2 is pretty safe and will work with a wide variety of Cobb parts(intake and full exhaust with a slightly bigger TMIC). You will notice a nice jump in power over stock with catback, the pull will be much smoother as well. It's also pretty easy to resell the APs on here and craigslist/eBay if you decide later you want to go further.
Like I said if your worried about 1/4 miles it's gunna come down to how fast you get off the line, I couldn't even run a high 12 with my 16g 02 wrx 5mt without nearly destroying the car off the line and it felt fast to everyone who rode in it including me.. So don't let times get you down. If your happy with the way the car runs, who cares what it does at the track. Especially being a DD, don't remember if you said it was.