Unfortunately, unless you get a guy that doesn't check your car thoroughly.. you'll fail visual
Personally, I'd say find some friends locally, and find a guy who will overlook the visual part as long as you pass the sniffer
Thats the gay part about CA - My regal passed BETTER than average in every category, but would have failed for visual on about 10 visual mods
I ended up getting a stang just so I could get all carb legal parts and not worry about it anymore
Your best bets =
Going back to stock every 2 years
finding someone who will help you out..
Good luck in either case
headers are a PITA on 99-04 cars!