These seems very simple recommendations, but:
1 - Have you verified that all/some of your intake bolts are not too long?
Almost every FE manifold uses different bolts and I keep a box of the ones I take out just because every swap I do seems to like something different. Generally, on the bench, drop the bolts through with the washers you'll run and 1/2 inch of thread showing is generally good. However, best is to measure the depth of the intake bolt holes because you don't want them too short and pulling out either
2 - Have you verified that the intake isn't hitting the head gasket tabs or the block?
I haven't seen it often, but I have had to take an angle grinder to bevel a 45 degree-ish cut along the length of each side of the intake. It can hit the head gasket tabs, and I haven't seen it, but theoretically could hit the block before it compressed the gaskets