I say do the mods that are fun first: Flowmaster cat-back, off-road H-pipe, 3.73 gears, shifter.
Then go for bang-for-buck mods: cold air induction w/ K&N, under-drive pulleys, Nitto Drag radials.
Then get the car ready for the bigger mods:
Intake: larger MAM, TB, intake
Exhaust...