the 5 liter has fuel injection, we have the fuel pump and the wiring harness
yeah we also have the tranny

You will need to upgrade the fuel lines. All of the other mounts should be interchangeable. The only other problem that l can think of is the hole for the pilot bearing if it is needed. There is the chance that the 89 crankshaft does not have one so it you are using a manual in the 66 there may be a problem. Just use the crank out of the 66, or get a new one that has the place for the pilot bearing.

google: 'mustang efi conversions'. ron morris is one of the pros. for the love of god, please do not put that engine in without putting good aftermarket heads and a cam in it, at least. jba and mac, l think, are the only exhaust manufacturers that make headers that actually fit with (i recommend) a replacement aod 4spd auto trans or t5 manual. your car needs overdrive so you can put a good 3.55-3.73:1 rear axle ratio. ''trust'' me on this.

If the motor is complete and you still have the donor car l suggest swapping everthing over including the computer and the trans especially if the trans is an AOD which will give great mileage. Fitting the entire motor and not swapping the trans might not give you the best results. It should bolt up to the original motor mounts my friend has a 64 Fairlane with a 5.0 which was swapped out from a 289. The swap works but you need a conversion kit from a Mustang retro shop.