Complete engine - pan to throttle body
Throttle cable
Air intake
MAF
Engine accessories w all brackets, lines, wiring, hoses
Motor mounts
Complete exhaust
Radiator & hoses
Fan
Overflow
EEC with harness
All engine wiring harnesses
Dash harness
Instrument cluster
CCRM (constant control relay module)
Hydroboost brake booster with all lines - the vacuum booster is too big and will not clear the 4.6
Transmisson - You need a 4.6 transmission. They had 4.6 specific bellhousings built into the case..... even on the manual transmissions.
Flywheel and clutch for T-45 and 3650 manuals
Flexplate for 4.6 auto trans 4R70W
Driveshaft - 4.6 has a specific yoke that is not the same as any 3.8 yokes. Tubes are the same length, in case you want to swap only the yoke.
Probably some other stuff. Unless money is not an issue, I'd sell the V6 and just buy a GT. Others will chime in. Welcome to the forum.