Did you have to rat tail the holes upward or downward to get the bolts in ? If downward a THICKER sealant is only going to make matter worse , you intake needs to be cut because it's not fitting properly , which is why you had to file the bolt holes.

If you had to rat tail them upwards then adding the thin paper gaskets between the pan and the manifold would have been the proper solution ... maybe on both sides of the valley pan if it was really low ...

Filing the intake bolt holes is not the right way to fit the intake.