Of course, the bolts/bolt holes have nothing to do with your real problem.

When you get everything cleaned up, do a fit test setting the intake on the heads, finger tightening the four corner bolts and checking gap size between the head and intake with a feeler gauge. Report back what you find. I frequently see intakes that leak, but yours looks pretty bad.

If you want to keep the dual quad set-up, you may want to consider getting the Eddy CH28 and enjoy a performance bump too.