Replace the cats correctly. Either with the original direct-replacement 2-chamber design, or aftermarket single-chamber cats.
The car is already built for peak performance with excellent reliability - mess with it & you'll probably lose some of both.
Open-element air filters are an advertising scam, like fuel line magnets. The Marauder filter box & '04-up zip tube help a little, but to get noticeable benefit, they require the larger MAF & a custom chip, which is a fairly involved mod. Not for beginners.
Loud mufflers are just annoying - they don't increase power, economy, or comfort.
If you want to change engines, you can make a Mustang 4.6L SC work, but a Marauder engine is built for this chassis.