My 2014 RT suffered the same fate. After the stator was replaced, the bike had new vibrations and a slightly different sound. In some ways, it reminded me of my 2009 RT when the throttle bodies needed syncing. The dealer's tech, a young guy with limited experience, tried to find the source but came up empty. The wet head has computer-controlled throttle body adjustments, so it seemed the 'out of sync' feeling must not be correct. To the service manager and the tech, the RT was within norms. It was not within my 'norms', but understood they didn't have a baseline: I did.
The bike was traded in and I moved into the R1250RT, a nice upgrade, but I was happy with the 2014.
A few months later, a new tech came along. I mentioned to him my issues with vibrations after the stator replacement. He pondered that, then asked if it sounded different as well. When I told him it did, he said that in putting the bike back together, care must be had in placing the airbox. The airbox can put pressure on one of the throttle bodies' control cables and subtly cause it to be out of spec and not noticed by the computer. An easy fix if that was the case. Too late for me, but maybe not for you.
I have no idea if that could be your issue, but thought it was something for you to look at.