Jason-
I'm having trouble understanding your transmission dilema. Is it that you can't decide or don't know what will bolt to a 302? If so, the Tremec T5 is by far the most popular aftermarket tranny to bolt in for the mustang crowd last time I looked. From Ford, probably the easiest to find will be the C4(3 speed) of the C6(4speed). Those trannies are in almost everything that Ford offered the 300ci straight 6 to the 351W or 351C. Maybe the cars that got the FE blocks had beefier C6's. I'm not sure.
Anyway, alot of these parts can be had for way cheap and to build them up or even rebuild them is way cheap, which you seem to know already.
As for the sheer weight of the block, if you can afford it, go with an SVO aluminum block. Don't know the price for just the block, but IIRC, a fully prepped SVO block starts around 5g. Don't quote me on the price because it has been several years since I've considered it for my F-100.
The frame can be easily shored up, I would believe, by simply adding subframe connectors or by boxing the frame. I know these cars are unibody and technically don't have a frame to be boxed, but the idea is the same. Lateral support throughout the length of the car.
Here's an idea, why don't we call up Jesse James and the Monster Garage and talk with the people they have come on the show. Or why don't we find some hotrodders that will be willing to lend advice and knowledgeable experience.
::poof:: off to find hotrodders ::poof::