What type of boost control is best for an automatic 99 RS with HRC stage 2 with FMIC? I was thinking just manual, since I wouldn't be adjusting it much at all. Also, what about a turbo timer? Are they nice? Which one should I get if they are good? And last, but no least, what kind of cat andwhat type of cat-back system?

If you are boosting under 10psi dont waste your money on an expensive electronic boost controller! Get a ball and spring (or make your own). As for a turbo timer anyone will work fine, but i guess you can find one to match your taste. As for you exhaust 2.5"+ would be best.. 2.25" is sufficient enough but you really want higher flowing exhaust. As for a cat im not running one, because i blew mine out when i was running to rich @ 5psi.
(shooting flames out the exhaust at night is kinda cool!!!)
But if you wanna stay within the legal spec, you can use your stock cat or upgrade to the Higher flowing ones.