If you are talking about the down load from the dealer it will basically just increase the RPM's before rev limiter kicks in. It needs to be EPA approved so air fuel ratio does not change. Adding a higher flow air filter means more air into engine and the upgraded exhaust allows it to be released quicker. So you will have a lean condition. Adding a fueler would be a better way to go to maximize upgrades.
Here is a similar problem:
exhaust popping.... - Harley Davidson Forums - HDTimeline.com
No, you don't need a dealer download, Bernie is right,:s you'll be spending money you really don't have to. With what you have done so far all you need to do is add more fuel, Harley's run lean from the factory and what you've done is lean it out even more. Read some of the threads on your question and you'll get a good idea on what you need to do.
Changing from stock exhaust and adding more air/air cleaner will lean it out. Keep in mind Harley's run lean from the factory so as to meet the emissions regulations.How did I make it leaner ? I just added the XIED which is supposed to make it run cooler, and the pipes came on the bike.