No... The gears will not throw a code.. If you have a warranty and lets say your posi goes.. when they open it up theyll be able to tell. Plus its a good idea to get the TA girdle and thats a dead giveaway if you put that on with the gear install. Even if you werent the one who changed the gear ratios they still wont cover it in the warranty.
Headers will void your warranty.. Headers might throw you a SES light for lean fuel to air mixture. So youd have to swap out the OBDII for an OBDI or swap out your O2 sensors for simulators. I dont think they have finished LS1 edit for labtop tuning yet either.
I was going to take BlkZ28s route with the exhaust but I was able to win my borla exhaust on ebay for 425 dollars. (Out bid the high bidder in the last 5 seconds and man did he send me some nasty hate mail).