The late engine bolts into the classic Mustang with no problem. If you wish to use T5 or AOD transmissions then you have to use late '66 motor mounts. Late '66 motor mounts are very similar to '67/'68 motor mounts but the upper hole in the '67/'68 bracket needs to move 3/8' outward. This modification is easily done. Simply set the '67/'68 brackets in position by inserting the lower bolt, hold the brackets such they are positioned correctly (saddle about forty-five degrees) and mark the spot where the bolt should go through (crayon works well). Take the '67/'68 bracket set to a machine shop, have them drill a new 3/8" hole for the top bolt, then heliarc a williams washer (very thick 3/8" washer) over the top of the new hole to act as a reinforcement). This costs about $50. Okay, to recap...if late motor with OAD or T5 then use these mounts. If you find '66 late mounts they will likely be $80 to $120 a set. If you find '67/'68 mounts they will likely be about $40-$50 a set, but you'll have to spend $50 to make them useable. What else?
Transmission. If you use C4, it will bolt up but you must use a custom flex plate. The original is the wrong balance. The only place I know that you can buy this part is from Windsor-Fox or perhaps NPD. If you use Toploader 4 speed, then you have to use the '69 302/351 bell housing, and this in turn requires a 164 tooth custom flywheel 50-oz imbalance (Ram Automotive makes one). If you use T5 then you'll need this bell housing, an adapter from California Pony Cars and a new crossmember also from the same company. An alternative T5 installation uses an adapted late model bellhousing and a new (but different) crossmember.
Accessory drive. You can use either the serpentine belt set up or the v-belt set up.
Serpentine: If you use serpentine, then you need to get a conversion radiator with the water inlet on the driver's side. NPD has these. You can use the EFI with the computer if you wish. Harnesses are available from Windsor-Fox. This installation is normally done with an aftermarket power steering pump if you have power steering. If not, I'm not sure about how to substitute the power steering pump. In the worst case, you can leave it in but cap it off so it does nothing but act as an idler for the serpentine belt. Ford Racing makes an adapter to eliminate the air conditioning compressor if you don't have or want air. Serpentine belt installations are fairly common but I don't have one, so I am only telling you about this conversion from memory.
V-belt. Use early timing cover and aftermarket harmonic balancer to use your original v-belt pulleys. You can remove the late harmonic balancer and timing cover and install your early timing cover in its place. The replacement harmonic balancer is a custom 50 oz-in imbalance item you can get from NPD. It looks like your original but it is balanced for the late engine.
The early intake manifold and exhaust manifolds fit or you can use aftermarket manifolds and/or headers.
The distributor must be late model. The early distributor shaft is too short and the gear is iron. The late engine has a roller cam and requires a longer shaft distributor fitted with a bronze or steel gear. Do not fit the old gear on the late distributor. If you do, the engine will self destruct as the cam gear and the distributor gear eat each other for lunch. The only distributor I know that fits all criteria is the Mallory Dual Points or Mallory Unilite distributors for late model 5.0 Ford engines. The part numbers for these are 2770401 or 4770401 respectively. Using any other distributor.s require more complex wiring to accommodate the electronics. Example: the late distributor that comes with the '90 engine will be the right shaft and gear but require you to add harness and module from the '90 car as well. This can get complicated and expensive. Distributors from MSD, Accel, Holly, etc., will have this same characteristic since they are designed to be used in the late model car. Simply put, the two Mallorys are the only easy solution.