I swapped a 78 motor into my 66 and there are a few things you will have to change....
A 78 motor had a ton of emissions stuff on it and should also have a air pump. The easiest thing to do is to set the 2 motors side by side until your 78 motor looks like the 65 motor
I removed all the emissions junk (including the air pump) egr valve, thermostat housing, plus some assorted brackets and the kick down linkage & brackets. Most of the newer motors used a rear sump pan where the Mustang uses a front sump pan.
You will have to reuse your 65 front sump oil pan & pickup tube & change the dipstick mounting location to the front position in the side of the block. You can plug off the old position with a piece of dowel rod.
A later style water pump will have a longer snout than the 65 pump so you will probably want to swap the water pumps and pulleys, brackets, etc. I used the later pump & dual pulley setup, but I'm running an electric fan. You might or might not have clearance issues with the later pump.
Also use your original thermostat housing in place of the newer one. The newer one has some emissions stuff on it.
The 78 head should have an egr valve mounted on the side of it. Remove it and cover up the holes with a steel or alumiunum blcok off plate. Use your original carb! The later model carbs are loaded with emmisions stuf and should be thrown in the trash!
Likewise toss the later model exhaust manifold in the trash and use your 65 one. The 78 motor will have a duraspark distributor. It can be rewired to run on your 65 or you can stay with your stock distributor. The Duraspark is a great upgrade though!
Use your 65 sending units.
Thats all I can think of right now!
Later,
Doug