Regarding the clipping....to me it sounds like the speakers are clicking a bit right before it cuts out. LOL, it's hard to tell for sure because I'm being deafened in my garage trying to replicate the issue.
Someone pointed out that the problem doesn't surface when the AVC is turned off. I'm not sure that's true, but AVC could absolutely make the problem worse by pushing speakers and amps that are already at 100% capacity over the edge. I think the quickest fix it to listen for the clipping and turn down the volume slightly before the amp starts cutting in and out. With any luck, Harley will update the programming for the amps to turn down the gains just a tad. Doing that would probably fix the problem.
Have any of you guys had other aftermarket systems in your bikes? How does the Stage II system compare to the likes of Arc amps Biketronics amps, aftermarket speakers (Focal, Polk, Infinity, Hertz, etc.)?