Newbie warranty question

Being new to street bikes and Harleys, I've learned a lot of great info and tips here from you all. But all the mods you are all doing makes me wonder about the effect on the warranty. I got the 5 year H-D extended plan, but would like to make some changes to the exhaust ( get rid of the cat ) and intake, and probably some sort of fuel management device. Can I make these types of changes and still keep my warranty in effect ? I know this is a pretty basic question, but I'd really appreciate your input. THX !