I can help..
When i rencently installed the 2013 motor on my 2012 S, i had to modify the rear wheel a bit to match the alignment of the 2013 motor sproket. In fact i machined the rear wheel sproket seat my 100 mil to accomodate the alignment of teh rear sproket. I playes alot to keep alignment perfect!
I had amisalignment at teh begining and snaped the belt!! at 8km from home!.. The angle diff between the two sproket was over 0.25 degree wich is the max tolerance according to Gates, the manufacture of these carbon belt. 64$ later and a new belt with proper alignment it is working like a charm!
If your belt is too close to the rear sproket shoulder, then you can remove the motor sproket and remove one of the spacer behind it. this is about 1.5mm thick and there is 3 of these . Then your belt should be 1.5mm far from teh rear sproket shoulder.