As far as I understand it (I could be wrong), if you do a modification, the warranty will only be voided if they can prove that your modification caused the problem. Personally, I'm going to wait until my warranty expires before I do any major modifications. Also, I should have the money to do modifications by the time my warranty expires.
Lycosa I would not worry about the tube for the intake. I have had my 2000 R/T in a couple of times for warranty stuff and the dealer didnt say a thing except nice dual exhaust. As long as you dont have any TBI problems. Like dirt getting in. Just make sure the tube is sealed good and you will be fine.