I believe the Tremec might need mods to the trans tunnel to clear. I haven't done this swap so I don't know for sure but I have seen guys have to slice and add clearance to fit this trans in a classic. The MII suspension is nice, A friend of mine did the Rod & Custom MII with R&P. The late model 5.0 has a "double" hump type oil pan and will work with most MII conversions. The 5.0 and the original 289 have the same motor mount points so that is not an issue. The late model 5.0 does have a water pump designed for serpintine belt (runs backwards to original 289) and use a cross flow radiator. You will need a cutom radiator with the bottom hose connection on the oposite side. The EFI setup will work but for best hood clearance the upper intake like they used on the T-Bird and last of the 5.0 Mustangs have a curved throttle body casting which clears the shock tower nicely as opposed to the typical straight HO 5.0 upper intake (both will fit however). If you go the EFI route you will need to modify the fuel tank for a return line as the EFI fuel delivery system is designe to circulate. If you decide to go with a carb keep in mind the late model 5.0 does not have a place for a mechanical fuel pump or the eccentric to drive the pump either. You will need to run an electric pump. If you decide to convert to a 289/302 timing cover, pulleys, water pump, etc. it will all bolt on and look like a classic motor but uses V-belts.
I recomend checking out JamesW website, he is a great guy and will answer any questions on this and other Mustang stuff.
EFI 5.0 install