Question about restoring and building a classic

why not 64-69?
From 64.5 to 66, the body styles were basically the same, except for changes in trim; 67-68 were also pretty much the same, with trim changes; 69 introduced other changes, but it still looks good.
I can't answer all of your tech questions, but I know that a T5 swap is very common. Front discs could be had on any model (coupe, fb, vert), but were a special option, hence much more desirable today. I don't think I've ever seen a classic Stang with factory discs (they were either upgraded to discs, or had 4 whl drums). There are many high-quality complete kits on the market to upgrade to front or 4 wheel discs, so I wouldn't limit your options by looking for a car with factory discs when you could find a drum car much easier. Also, if you're going to be putting 347 power into the car, you'd be upgrading the entire brake system anyway, I'd think.
my 67 coupe is rated at about 2880 lbs, but I don't know how realistic that is.
Going rate? depends on your location, and the condition of the car. a straight body, rolling car (no drivetrain) could still command a few grand, depending on its condition and location. I'm in Miami, and a classic Stang in ANY condition down here brings big $$, from 2-5K for a rust bucket coupe to well over $20K for a nice vert or f/b.

with the amount of changes that you're looking to make, you could pretty much start with any solid car. hell, even a 6banger car with a decent frame would be a good starting point. the T56 will go in, but you'll have to hack up the transmission tunnel and fabricate another one. find the best body you can and start replacing everything.

you wont get the weight down to 2500 pounds without a LOT of fiberglass and very little interior.

ok the t5 will fit on the 64.5-68 but to get the t56 to fit you'll have to go with a '67-68 car. a t56 was put into a 64.5-66 car, but it took some modification to the transmission tunnel, you can check it out at www.totalcontrolproducts.com

as for the new 5.0 blocks being similar to the old small blocks, i currently have an '89 5.0 HO mated up to a '66 C4 automatic without any special adapters

the blocks will all bolt up to each other but the newer 302 blocks are full roller blocks whereas the older ones are not. the t-56 will fit but will require pretty extensive trans tunnel work. No stock discs on an old stang will be sufficient in reality so I wouldnt worry about that

Baer and SSB both make nice brake kits for the 65-73 cars. If it is mostly a drag car, Wilwood also has some offerings but they are not suggested for daily drivers. In any case, the stock discs measured in at 11 inches with puny calipers and a single pot master cylinder. Brake tech has come a long way!

For comparison, Chevy was more than willing to send you out the door with a 396 SS Camaro with drums on all four corners. All of the manufacturers did that back then. Probably the scariest from that time period was the 426 Hemi's in a heavy Charger with drums. Can you say FADE! Scary!!