I've been warned by several people (including Ken at Cycle X) that the stock studs tend to stretch, which would lead to a head gasket sucking air from all the wrong places, and leave you right back at square one (pulling the motor). That was the reason I had to do the top end on my motor the head gasket was sucking air around cylinders 3 and 4. But I'm always willing to learn and listen to anyone who has new information, but it makes me feel a little better about usuing the stock studs.
Since I still have to paint my frame and other parts, I'll have to pull the motor anyway so I will probably check them just for good measure. And no my frame is not cut for clearence, but there is usually plenty of extra help around the shop for motor pulling.
Travis