hdhighwayman,
Great question and I got the feeling that some HD Dealers are OK with Power Commander and others aren't. I know the Mo Co is trying to keep the 3 letter US Gov Organizations all happy and aren't as easy to get info on. My feelings the few modifications I have done with my bike should not cause any/many problems in the future. As a matter of fact I think what I have done will actually make the motor run better.
Keep your stock exhaust and such - who knows what the 3 letter US Gov Organizations have in mind.
As far as Extended Warranty, I would have the "big boy" discussion with your HD dealer and get his feelings on this subject before I went with to much of a extended warranty. I did take out the 3rd year and I now have some regrets but I wasn't sure about the new Stereo and such. My take on extended warranty is, chance's are I am not going to keep a scooter more than 3 years. So I now don't go for the extended warranty any longer.