Nothing if you buy the appropriate kit.
I mean i have a low boost Paxton Novi 1220SL on my completely bone stock (engine) Fox mustang. It's their 6psi kit. I upgraded the fuel pump, had my injectors cleaned out/repaired, put fresh spark plugs and gapped them down a bit from stock. BUT, the kit says it will work on a completely stock Fox. I'm sure they have similar type kits for the new edges.
For tuning though... i have no idea on newer mustangs, especially v6's what the computers can/can't do when adding forced induction.