Are you going to consider fuel injection or no? If yes, in addition to the Mark VII years Tech suggested, also look at the '89 to 93 Mustang GT's. I think '85 was the last carbureted 5.0 in a Mustang. '86-'88ish used a speed density fuel injection and '89 they started using Mass Air Flow style, which is better.

Any of the 5.0HO engines found in Mustang GT's, Mark VII LSC's and some Tbirds will have more horsepower than the non-HO. Ford Racing offers a plugnplay wiring harness for installing these fuel injected engines into older cars. It connects to the existing wiring harness. I f you don't want to consider fuel injection, you could swap the intake to the carb style. A while back I put a '92 Mustang EFI 5.0HO/AOD in my '66 Ford pickup. Once I got everything sorted out, I totally love it and want to fuel inject everthing!!

Many of the later 302's use an electric fuel pump, so you'll need to consider that, too, and the fuel injection requires a return line to the fuel tank.

As for AOD's, they got much better in the late 80's early 90's so I would gravitate to those years.

Isn't the '59 chassis basically the same as Galaxies up through '64? If so, Ford offered a 289 from the factory in those cars so I would guess the same style motor mounts would work for your '59.

Anyway there's some initial food for thought. Hope that helps a little. We can provide more input as we learn more about what you have in mind.