Some 305s and 350s had different spacing on the manifolds/heads at one end of the head. I have no idea why. Maybe you have a mismatched combination of heads and/or manifolds?
The replacement crate engines like I bought are drilled for both types of manifolds. Take a look at the pic below. You can see how it is drilled for both types of manifolds.
Is this the part where you are having problems? If so, that is probably the problem. You probably have a 350/283/307/whatever with 305 manifolds.
http://www.crateenginedepot.com/stor...6041_large.jpg
Slonaker