Hal, I just bought an 09 FLHX and when I ask about warranty they said that as long as the HD dealer does the upgrade work they will warranty it. If I buy the parts at the daeler and I put them on, like Rinehart mufflers that I bought they would also honor the warranty. Bottom line is it's up to the dealer. I was thinking of the 103 kit and was told that if I have the upgrade done within 90 by the dealer that it also is under warranty.
If you think they might not honor your warranty you can reverse the mods on your bike before bringing it in. The ones you listed should take less than an hour to do. When you get home you can slap them back on. (you didnt hear this from me)