From what I have read, the Stage 1 kit will still run clean enough to pass a tailpipe test. We don't (currently) have vehicle emission testing here in Michigan, so I don't have any personal experience with this issue.
The warranty question could be more complex I think. We bought our '03 GT from the original selling & servicing dealer as a Chrysler Certified Used Car, and since the dealership installed the kit (+ BOV) for the original owner before they traded it in it's all covered by both the factory warranty and the extended Certified Used Car warranty as well. Now, according to them if we subsequently purchased the S1 kit and installed it ourselves it would not have been covered....and in fact could have lead to 3/36 warranty problems as well.
I would talk to your dealer about it and see what they can do for you
Brian