2009 nightster not running smoothly. Chokes down, sputters. What could be wrong? Read on?

The collar around the rear exhaust came loose. One bolt missing, the other loose. Harley dealer replaced it and said I was good to go. My bike has not run properly since same dealer did stage 1 and screaming eagle pipes (tips) about 5500 miles ago. They continuously told me there was nothing wrong. Now they have fixed the exhaust leak but when I asked if they did a compression test or checked for burnt valves they told me no reason to. Said my problem is I only did the download when staged and pipes installed and that with screamin eagle pipes I have to either put a super tuner or power commander on bike for it to perform properly. They still will not do compression test or break open the heads to check my valves. Common sense tells me I'm getting screwed. I know there's a possibility of burnt valves among other things. Am I wrong? Is the super tuner or power commander necessary or should I keep fighting them to do compression test and check the valves before I take the bike back? They told me I could come get the bike and ride it for a while and see if there is any difference in performance but I'm pretty sure my motor has sustained damage. What can I do?