Get some machinists dye and find out if the intake ports and bolt holes are lining up. If they aren't, you will need to either have the intake or the intake side of the heads shaved down so everything lines up.
Sounds like his issue is not that the bolt holes don't line up, its that the bolts hit the runner when trying to install them. It's an issue on the super victor, and other intakes for sure. He can get the 1-1/4" bolts in, but the flange is too thick on the intake so that only leaves three threads to engage.
