GAAAH! (rips your head off)
uhh....no. 3.8 is not in any way affiliated with a 5.0.
anyway, OP-
1. an M90 will NOT fit a 99+ mustang. the only way is to convert to a singleport setup, but this is taking one step back to go 2 steps forward.
2. fix all the problems first. suspension, body, brakes.
3. comp[ression check. if the engine is unhealthy, dont bother blowing it.
THEN think about making it faster.