sbtc,
From your research, you have probably determined that the proper procedure for the surfacing of the manifolds would be bolted together with a new gasket and machined as "one"! If it was done in this manner, it must be right.
If you can loosen the four bolts connecting intake to the exhaust, and re-tighten the exhaust manifold to the head and get rid of the leaks, then the machining was not done correctly.
This is a straight forward mechanical seal and no goop is necessary. Poke around and you will probably find the problem quite easily.
Stuart