Do a search in this forum for 'rsw007'. He runs 13.00's with very minor engine mods (intake, bigger valves in stock heads, factory headers), and the big key for him seems to be his tranny mods (stall convertor, shift kit) and a tranny cooler to keep it healthy.
His car is more the exception than the rule, but you shouldn't have any trouble getting into the mid 13's with afformentioned mods with the 3.73's you're planning on as well.
Yes, I know. But I HATE automatics in performance vehicles. This is the first automatic Mustang I've owned. And the only reason I bought it was, it was super-clean with low miles for cheap. I already have a Motorsports Super-duty T-5 in my garage. I'm just looking for an excuse to put it in.
I like manuals too, but to be honest, a prepped automatic wins races. You never miss a shift and are more consistent. So if you are serious about winning then build a decent auto, if not, then just throw the manual in and have fun.