The trannies are totally interchangeable. The only one to avoid is the one that came behind the six-cylinder in Chevy pickups. I think it had such a granny low gear that the shift from 1-2 would be horrible.
I don't know too much about them, other than that they are lighter duty than the Muncie four speeds. They have a steel case, so they tend to be heavier.
You're right about adding inches. Join the "L-list" at the bottome of this page. There's a really cool thread going on about upgrading to larger motors. It's basically about economics. You can invest a lot of money into a 326 or a 350 to get them to haul a**, but that same money into a 455 will get you a motor that will scare the ... well, you know.
My advice ... which you didn't ask for ... is to build a relatively mild big-inch motor, and spend the money on a great paint job. Tom's head/cam/intake/carb choices will let you do exactly that. But MAKE SURE you start with a sound bottom end. I build my motors like Tom does, though our opinions differ slightly when it comes to intakes and cams. But they are just opinions. The best bang for the buck is a motor with tons of torque that you can drive anywhere on pump gas.
