I just got my back back from the dealer fixing the inner primary bearing for the second time . This time after dealing with HD moco, they fixed everything, tranny case, inner primary case, etc etc etc.
Drive it ten miles today and the engine light comes on and stays on.
UGH !!!

 

Bet it's the Stator.. My bike has been in for almost 3 weeks for the full IPB fix, same as you.. I've really been buggin them to closely examine the stator and Rotor. Really has me concerned. Of course they havent heard of any problems with the electrical systen on these dynas.

 

Turned out it was a sparkplug wire.
I been reading some post about dealers charging $100 for the inner primary fix when it is out of warranty.
My dealer did not charge me anything.

 

Shoot I don't have a dealer anymore so I went to the next town that had one. They played dumb and I wasn't into the long distance fight for warranty state of mind so I did the baker bearing and called it good. Glad you got yours covered.