Knowing that there are variations but this is my observation:
Holley 1946 does not bolt directly on your '65 head. It does not even bolt direcly to a late-200 head like an E0BE '80 head. Ford used an adapter plate in between, like this:
http://www.ponikorjaamo.com/ti80/fsp/e0be-9a589-ea.jpg
As David said, the bore is 1.75" so it'll need mods on the head bore and the way it is attached on the head. If you have or get that adapter it goes easier (regarding the attachment).
Linkage needs mods; mechanical vs. cable. Here you can see the cable coming to the carb from the firewall, and it attaches to rear of the carb (the other cable is cruise control, if you wonder why there are two). If you are going to cable throttle anyway this is not a problem.
http://www.ponikorjaamo.com/ti80/ti80_eb2.jpg
There is a special metal bracket that attaches to the block and to left carb mounting bolt. It would be handy to have and I'd pretty much guess that with it a '80 Mustangs cable linkage would be "bolt-on". The bracket can be barely seen in the engine pics; starts at the coil and goes all the way up and between cleaner and valve cover to the carb bolt.
I had a round '65 style air cleaner just a while ago = it does not fit on a 1946 which requires not-so-flat cleaner base as the top of the carb and especially the choke requires space upwards near the bore:
http://www.ponikorjaamo.com/ti80/fsp/holley_1946_1v.jpg
Compatible cleaner looks like this (sorry don't have a pic of the base but I can take if you wish):
http://www.ponikorjaamo.com/ti80/fsp/gen1_engine.jpg
The cleaner has temp/vacuum switches that close cold air intake and take heated air from the exhaust if the weather is cold. Nice, prevents icing.
What comes to 1946 in action I'd say it was the best carb overall that I have had in my '80. Once it was refreshed with a rebuild kit and set up correctly it worked great in all conditions (-30C - +30C tested). I had all the pollution stuff taken off and PV spring modded lighter but there was no evidence if it had an effect or not. Got about 25mpg on stock 200000 mls engine, about 22-23mpg on rebuilt GEN1 112hp engine.
Carb swap alone is questionable, but if you want to go that way go to your salvage yard and grab an E0BE head, 1946, adapter, cable linkage, cable bracket, air cleaner assy, Duraspark II dizzy, module, coil plus plug wires and there you go...best factory Ford USA 200/250 head/ign/induction setup and works nice after you rebuild the carb and head, toss the module and put a MSD6A in and gap the plugs to .050. Well is that questionable? Sorry long post.
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