Sounds like, with the exception of the engine, your drivetrain is set up like mine!
I just finished rebushing the parallel 4-bar rear suspension...it was a difficult job, the first time I have ever done anything like this, but the car now rides SO MUCH better and, wonder of wonders, there are no more rattles. I really like the way the car hooks up with the 4-bar suspension in the rear (I also have a Panhard rod...that was the worst part of the job!).
My 9" Traction Loc is indestructible, Lord knows I have tried!
Without doubt the weakest link in your drivetrain will be the T-5! More durable models are available if yours is a stock Mustang T-5...but, having said that, I have had no trouble with mine (despite having 295/50X15 rear tires that are 11" wide), because the Cobra is so light that the tires break loose before the transmission is stressed.
I well remember your "innumerable" threads during your due-diligence phase, littlewave. It sounds like you were well prepared for the car you eventually bought.
Good on ya!
Cheers!
Dugly