I droped an 88 GT Fuel injected 5.0 in my 1967 mustang, and currently i'm running the stock shorty headers and H pipe from the 88 but i get a slight rub on my tranny mount from the H pipe... i was thinking about swapping out the shortys and H pipe for full headers and x pipe designed for the 67 body style.. will this screw up my fuel injection???

This will work, as long as you keep the O2 sensors, and install them into your longtubes. You will (depending on which set of headers you buy) have to extend the wiring for the O2 sensors or they won't plug in. The X-pipe should work ok.

ok thanks... someone told me that the exhaust was specialy tuned for the FI and i had to keep the stock headers and H pipe. any suggestion on what headers i should go with?

There's a lot of options out there for headers. So that will mostly be up to you choosing who your favorite brand is. But some things to consider are whether or not you want equal length or unequal length, and Jet-Hot/HCC coated or not. Equal length headers give you more power, and if you're willing to spend the extra money (which I would reccomend) make sure the headers are Jet-Hot/HCC coated. This disappates the heat more effectively to help keep engine compartment temps down. Just some things to consider. Good luck!
-Paul