Don't waste your time taking off aftermarket parts!!! Read up on the Magnuson-Moss Act. I work for an aftermarket supplier (
www.k40.com) and we run up against this all the time with BMW dealerships. It's a fear tactic. The dealership has the burden of proof that the parts you installed were DIRECTLY responsible for the failure of the warrantied part.
From what you mentioned were faulty, there is no way the exhaust and CAI caused the failure. Go in and tell them right from the get go that you know about Magnuson Moss and that based on it, your mods didn't affect the failed parts. You won't get messed with. I had mine in for a week for the hard start when warm problem. No charge and they replace the fuel pressure regulator and flashed the PCM. Helped a little...but the turn the key and prime the injectors is a better fix.
Dealerships don't like warranty work. They only get 1/2 or slightly more of regular labor rate as reimbursement from manuf. That's why often it takes several trips back to the dealer to get warranty bugs worked out. They want to spend the least amount of time fixing it each time if full paying work is backing up.
Don't come off like a jerk about the info...just be knowledgeable and polite and you'll get taken care of and not waste any time. Besides, the tech like to see what these cars sound like and run like with these mods. They were pretty surprised with the torque gains on mine.