Yup, it's common for the aftermarket pumps to not fit quite right. The problem with the pulley rubbing on the casting can usually be solved by grinding away a bit of the casting mark on the casting.
However, the pulley rubbing on the studs sounds more serious, since it also means the pulley is too far to the rear. Although it would work, the belt will wear faster if the pulleys aren't lined up. There were also some early versions of the "improved" pump where the shaft could move in the bearings and cause the seal to not hold water. I'd wait for Monday before doing anything else, as they may not take it back if you have been grinding on the casting.
As a side comment, it is important that the pulley is a very tight fit on the shaft. If you can just slide it into place, it will eventually work loose and tear things up. I've used Loctite "retaining compound" (aka "Circular parts mount") with some success, but of course it will make it harder to disassemble next time.