There are a lot of threads on this website on whether to buy a 4.6 or 5.0.... Check them out and see if they help you out...
There are 2 main reasons I bought a '94 GT (302ci) instead of a 4.6: 302's are much easier to work on, and aftermarket parts are cheap and you can find them EVERYWHERE.
In my opinion the only advantage the 4.6 guys have is ease of tuning with a handheld tuner...
A lot of "GT guys" actually upgrade their heads and intake to a Cobra setup. With the GT40 heads and GT40 intake.
Why do people buy the Cobra? Well, because it's a COBRA!

Most people tear into their motors whether it's a Cobra, GT, or V6. More power almost always equals more fun!
If you want to make more power, then you'll have to change things. Gears are the best bang for the buck. They are fairly inexpensive and will give you instant gratification. Something else that will make you quicker at the track would be to upgrade the suspension. Get some subframe connectors, upper & lower control arms, and some good shocks/struts.
Another way you can make more power and keep all your other stuff is to stroke the engine to a 331 or 347. Why in the world would you want less displacement?
The 4.6 is a completely different engine. It's and overhead cam engine compared to the pushrod 302.