I'd take it all apart on the alternator side and see what's up. Did you install the engine? On some aftermarket heads one of the bolt holes on the passenger side cylinder heads has to be tapped a little bit to get the bolt to go in all the way.
Kurt
Yep, I installed the assembled shortblock into the car, as well as all of the accessories including this bracket. I wasn't aware of that some aftermarket heads required tapping some of the bolt holes, but this is certainly a place to start looking.