Help with Novak SS13.5 dissassembly

This probably sounds stupid, but I need to sort this out so if anyone could give some insight on this it would be greatly appreciated and I know you guys are the brushless gurus so hopefully you can help.

Ok here goes, I have a Novak ss13.5 system for my 1/10 pan car, I picked the motor system up used and it runs great, however one of the mounting holes is stripped out, of course its on of the ones I need . Anyway there are multiple different mounting holes on the end bell, and three screws that bolt it on so I thought (always a bad thing) that I would just rotate undo the end bell and rotate it to a different orientation so I could get a new mounting hole. Well I did this and now when I spin the motor by hand its very notchy, much like my Neu or my Medusa, like you can feel the poles on it, it was never like this before, it would spin very smoothly by hand. Did I do something wrong, should I have not tried to clock that peice without changing endbell orientation as well?