Your nuts!
Just mod the Mark. It'll be faster and ride 10 times better than the Trans Am. And if you throw some 17-18's on with some nice tint and lower it 2", it can be a pretty badass looking car.
You can toss a used Vortech (or simliar) on there and run 6-8 psi and see close to 350-400 to the wheels. What is wrong with that.
You can start with a J-Mod on the trans and then add some 4:10's and a Trac-loc. The list goes on and on. The 4.6 market is just starting to come of age. If you pull your motor, you can use the shortblock as a core charge credit and pick up a new built shortblock for about $2K with the right pistons, rings and rods and really go to town. With the right shortblock and some larger injectors, 500 rwhp is easily within reach. That will make you forget all about the TA, I guarantee you. Keep the "b" heads you have and have them ported. They flow pretty well. The Gen 1 intake is also good for a blown application. Ford did almost everything right with this car except for the pistons, rings and rods. Even the cast crank can hold alot of hp. I might toss on a high performance oil pump to keep things lubed but I would stay away from the billets that are just too hard and have a tendency to walk and do some grinding.
We need more guys modding these cars, not selling them off to go backwards in time. In 20 years, these will be the cars to play with, I'm pretty sure of that.