CRAP! I'm smoking!

I always fit the intake as an assembly procedure. You want the bolt holes to be biased towards the top of the bolt holes, but fully visible with no gasket. I use the Mr. Gasket Ultraseals with sealer on the end rails and that always seems to work well. Sounds to me like the manifold just doesn't fit. The valve seals "may" also be an issue but I think it's the gasket predominantly.