MLS head gaskets are not very forgiving to an imperfect surface. It's possible they can weep if the block and heads weren't specifically surfaced for their correct finish. Unless you're running boost they're also overkill. A composite gasket with stainless fire ring like the 17068 should be a good fit.
I agree that silicone on the head gasket is a no-no.
A light silicone smear around the water ports is a good idea on the intake and corresponding mating surface on the heads, with the intake gasket between the smears
