It is unfortunate you already spent money on that 727. An early 90's 518 transmission out of a dodge rwd truck/van would be the ticket for you. It's basically a 727 with a .70 overdrive gear. It will bolt straight up to a small block (perfect for that 408 stroker idea of yours) or mate to a big block with an adapter. The 518 could be made to fit under your car with a minimum of fabrication(shorter driveshaft, custom transmission mount, possibly some crossmember modification. Also the 518 has a superior overdrive gear to the .80 on the gear vendors. With the 518, you could do 4.10 rear gears and on the highway it would drive like a 727 with a 2.87 rear gear.

Either way, I would get your transmission choices nailed down, and worry about the rear end later.