You'll need to address the fuel system (return in your car vs returnless on the newer motor).
You can get everything you need from Super Six Motorsports.
1998 Roush: M112'd Aluminum block 4.6L 2V 6 speed track car
1999 SVT: Mostly stockish
1970 Mach 1: Resto-modded monster
2000 Roush #5004 - World's FIRST M112'd V6 Mustang. Sold, but not forgotten.