you dont wanna upgrade things that are gonna be too small once/if you decide to do more upgrades, by this I mean dont buy a 65mm TB/EGR then later on relize its too small and you want a 70 or 75mm unit.
94/95 Mustang MAF. The stock MAF is 55MM and the 94/95 is 65MM. I just sold one on Ebay for $50.
K&N air filter. The stock filter and housing is already a cold air system. Just remove the silencer (+3 to 5 HP) and add a K&N.
Under drive pullies...
Bump stock timing to 14.
Install a indexable timing chain and retard the cam 4°. This gives the car more top end HP.
It you want to upgrade the shifter just remove the rubber bushings and install metal sleeves. 99% of people have no real clue how to shift (just watch some Youtube videos if you want to learn how NOT to shift) and they don't hit the shift arms hard enough to bend them. I would only change shifters if I were having a problem with the 2-3 shift. I have a buddy with a 70 Dodge Challenger that makes at least 100 more HP than I do. I kill him every time. He has one of those funky old Hurst pistol shifters and it takes him forever to get from one gear to the next.
Rear gears are nice but the performance increase is marginal given the cost to have someone put them in. It's more of a mental thing than anything else. I would do them but they wouldn't be first on the list, especially if you already have 3.08 gears.