Pulling the 289 and dropping in a more modern 5.0 is the most straight-forward way to do it. Everything bolts in, but you will need the proper flywheel with 50 oz of unbalance to replace the 289's 28 oz flywheel.
I have done 7 of these swaps now, and the wiring really isn't that hard. I have it down to a science where the whole shebang comes down to two wires, one power and one ground. It is a bit of work to get there, though.
The EVTM manual (Electrical and Vacuum troubleshooting manual) for the donor car is worth every bit of the $40 it cost from Helm publishers. It is a lifesaver when it comes to wiring it all up.
there is a lot of wiring involved with a swap like that. I don't know if you can even get the necessary sensors to fit properly on the original engine without taking it out and doing some machine work. It would be a big job and then the car would no longer be original.
You might be better off getting a wrecked mustang with the injection system on it and swapping all the parts. But for Pete's sake keep the original engine because one day you might want to restore the car.
Best bet is to get a wrecked Mustang with the whole fuel injection system still intact.
Wiring is simple with a schematic and taking your time.
The hardest part of the swap is running new fuel lines AND The fuel pump has to go in the tank too.
There's alot of aftermarket companies that have gas tanks ready to go etc. for using fuel injection in your '65.
the 5.0s that came in later year fox bodys are your best bet tho you will have wiring mods to do. Lots of wiring. Plus adding sensors in quite a few palces. Best bet is getting a complete donor car and a guru on wiring and swapping entire drivetrain and wiring from old to new. Good luck but lots of people have done it. The old style (mech. inj.) is even more expensive and prob. offers no gain for the street.