I would get a built tranny first, then do the lil mods as you get extra money. That way your tranny will hold up and with just over 100k your motor should hold up well for a while.
I am also in the same boat with my mustang, couldn't afford a cobra and got a gt instead. 15k for the car ,15k in mods and I would be lucky to get 12-14k for it. GRRR