Hi,
I'm the guy with the ape's and darkside tyre, not sure whats going on with mine either, but it sounds very similar, mine is also a 2011 r3r, on the second reg now, the sparky put a 35 amp on it now, I have since removed ape's and fixed some wires in there that looked suss, moved the reg to under the headlight where the horn was, put a little heavier wire to join it all up, seems ok, but the abs light has come again, last time it done this it seemed like the reg died, but not sure this time, tested out fine but, charging the battery at 13.8 volts which has increased from 13.4 before the abs light had come on, i'm now at a loss to what the problem could be, I would be interested in finding out what your problem is.