Couple of facts... K-members did change in V6 cars in 96 along with the GT so you will need a 94-95 member. Also you will need the harness and computer from 94-95 V8 car too.. You will need to replumb the fuel system since the 99+ V6's are returnless (which includes new fuel line, fuel pump basket, etc.). When you go with the 94-95 computer and use your stock T-5 (which the 99+ V6 T-5 is a stout stock T-5), you will need to swap tailshafts and convert to a gear driven VSS. The bellhousing pattern and depth is the same as 94-95 V8's.
Then.... you start into the particulars that do with the engine itself. Like it was said, a 95 or older would be a better starting point. You have significant things to overcome just to get the car to the point to start the swap.
1993 5.0L LX Mustang
GT-40P's, Explorer Intake, 5-lug swap, PBR Brakes/Rear Disc, 3.73's, SCT Pro-Racer, 80mm Lightning MAF, 65mm TB, 17" Bullitts, B-Springs, MAC LCA/UCA's, X-Pipe, Magnaflow catback, Elect Fan, more...