1. Everybody has their own ideas about mufflers, and truth is there are just way too many flavors to choose from. This also depends on the exhaust set up as a whole, not to mention gearing. If you want quiet, then by al means go ahead and get a stock replacement muffler. If I'm not mistaken, flowmaster, magnaflow and the like all make stock replacement sounding mufflers as well as the performance mufflers.
2. For the brakes, Id try ugrading the brake lines and getting performance pads before upgrading the rotors and all that. Here is an excellent write up:http://mustangforums.com/forum/wheel...wing-down.html
3. A lot of people (myself included) agree about the aesthetics of the suspension set up. No matter what you do however, there will be a trade-off for some ride quality on some level. There are however some mild lowering springs that will not make too much of an impact on ride quality. Don't go more than 1.5 inches, or it will be noticeable for sure, plus C/C plates would then be a must for alignment. Although they aren't a bad idea on a stock ride height car either.
4. Any mild modification will net you nearly nothing on these engines. Your best bet would be a PI upgrade, but that means upgrading the heads, cams and intake to the 99-04 versions. Consider upgrading the gears. This will be your best "seat of the pants" upgrade. You will feel it for sure, but it leaves your engine alone. There are lots of different ratios available. Take a look at Americanmuscle.com. TONS of options there, plus you get a 6 percent discount for being a forum member here! Hope this helps, and Welcome to the MF!