I've read on the SSP forums good things about the Dynomax exhaust systems. IIRC, you can purchase all-new parts from the header/manifold rearward. I went with a Thrush system on my 85, with hi-flow cats (one of the four cats was plugged up), and a new h-pipe. Here's a cruddy cellphone pic I took before he cut off the ends of the u-bolts -
The sound is quiet at idle, with a nice tone upon accelleration (not as loud as Flowmasters I've heard).
My car also has a 93 Cobra 8.8" rear in it (installed by a previous owner), with 3.27:1 gears and 4-lug disc brakes. I've got 11" 87-up front brakes as well, and the car stops as quickly as the tires will allow. If you do change out the rear, my suggestion would be to keep the original in case you ever want to put it back to stock.
As stated, it's your car to do with as you wish. It sounds like you have a good plan that won't sacrifice the SSP heritage that makes these cars so much fun to own, drive, restore, show, and/or enjoy.
EDIT: And those awful subframe connectors will be coming off my car at some point. They're so flimsy I can't imagine they are doing any good.