Unfortunately I can't give specific help... but what I would do in your situation, is first establish, is the roughness felt in all BWR gears? Sometimes geared hubs may impart a rough feeling especially more so in some gears. If that draws a blank, backpedal or pedal on some sort of back wheel off the ground setup and try to spot what rubs to find the culprit. The only one I can think of is the derailer actuator rubbing against the chain but you have already eliminated that, I understand.
Thanks for the suggestions. Yes, the roughness is felt in all BWR gears when the chain is on the large sprocket, but not at all when it is on the small sprocket. The funny thing is I don't feel the roughness when backpedaling (in the large sprocket).