I've experienced the same thing, I have my stage one air cleaner, just haven't installed it yet. On my previous bagger a 2012 Ultra Classic I did the same upgrade. Installed new slip on mufflers and a stage one air cleaner. After getting the download at dealership everything was good. Just lost about 8 mpg on the fuel side.
I Ride: 2014 Ultr Limited, 1950 FL Panhead
10 months ago