[sick472]

Sounds like a solid plan to me even though I hate to see you have to take the intake back off. I would make sure you have the correct length intake bolt before getting into the big picture. To little thread engagement and the sealer may not be able to do its job, too much and you bottom out on the end or shank before gaining proper grip from the applied torque.

I have only built a few engines, but I have always used Black RTV high-temp in the bolt holes that go through to the water jacket...never had any leak.

Of course, your leak may be from the intake gasket itself and Jamyers has you covered!