I don't know about having a manual transmission shift that way, but I do know a few people that have automatic transmissions with manual valve bodies. This way you have to shift the automatic like a manual. There would be no clutch pedal but you would get your straight line shift pattern and it would make the transmission swap easier because you would not have to install a clutch pedal.  C4 and C6 transmissions would be the easiest to match to a small block ford and I know that summit racing and jegs sell the manual valve body conversion kits for both.
 
As for the rear axle swap depending on the year that you got the 9in out of, it could be a direct swap. If you want it to look stock I wouldn't worry about tubbing the rear. You can fit some pretty fat tires in the stock wheel wells.  You could also use a product called CALTRACS to help eliminate wheel hop, and gain some extra traction from your leafspring suppension.  If you really want the super fat tires then I would consider doing a tub and four link suspension.  This set up also lends itself to installing a roll cage for safety.  Either way you go, I would highly suggest doing subframe connectors to make the unibody more rigid. You don't want that big V8 to twist your cars body if you have taken all the time to swap the engine.

Hi,   I guy who lives a mile from me is doing a 302 into an early pinto and he has moved the front end (cut it then welded it back in) for better performance and also used the rear end out of a ford explorer by shortening it then bolting it in.  Said it will be beefy enough for the punishment.   I can get more info and maybe pics too next week if you want.