Darn me if those HD engineers don't know what they're on about. I am one of the few who have these on my bike, just replaced them with the stock mufflers, with less restrictive (louder) baffles. The result: noticeably less torque and power at all RPM's. Must be a back-pressure thing. Guess they do know what works. Too bad the SE's sound so wimpy (plus they're fugly).

 

So let me see if I understand your post.
Your bike had the legal SE slip-ons first. You removed the SEs and put on OEM stock mufflers. OEMs were quieter and lessened performace of bike.
Question. Why did you remove SEs?

 

I have a set of the OEM muffs with different baffles made by American Custom. They are louder and better looking than the SE's. I might switch back, someone, I think Cycle Shack, makes louder baffles for the SE mufflers. I guess my point is slip-ons are not all created equal, they have to be designed correctly internally for performance gains. My bike was stronger with the SE's but popped and spit a lot even with the HD Stage I download and XIED's installed (have SE air cleaner also). no such troubles with the American Custom modified mufflers, but reduced performance, much like dead stock.