Intake swap

Most of the time, the intake gaskets have their own sealer already applied. It'll show as a bright blue or red "bead". If not, the surface of the gasket is a special material to allow for expansion and contraction. Personally, I'd leave it alone and let the gasket do its job, especially if you have an aluminum intake on iron heads.

The end seals can cause misalignment of bolts and make it difficult to get the manifold to seat well on the heads. Leaving them out and applying a large bead of RTV makes the job go much more easily and seals better than the cork, which tends to slip out. Place the intake on immediately, and torque to spec. Allowing the RTV to set up can cause more problems than I can list here, but the worst of them are leaks and possibly breaking an aluminum manifold.

Any bolts going into the water jacket should have sealer of some sort on them.

Hope that helps.