I repainted a set of Gils. They had thick powder coat on them. I tried to sand the exhaust surfaces clean before painting them. I know that I tried to feather the bare metal into the powder coat near the mating surface. This has caused a recess, maybe 1/16th of an inch on 2 ports. It looks like the exhaust manifold was leaking in these areas. Can a machine shop resurface the mating areas? Should I try it my self with a sander or file? I don't want to mess up the great paint job I paid for with them.

I always use a belt sander on old manifold runners. Even the mating surfaces of some new manifolds. Just make sure taking off some of the runner material will not cause other issues like the manifold hitting the valve cover.

You can mill the header surface slightly but if you change the flange angle much your tailpipes may also not align at the transom.

We have them milled, and have found the Mallory Marine exhaust manifold gaskets are better than the OEM for holding up against blown exhaust manifold gaskets plus seal better. Mr. Gasket makes all of Mallory Marine gaskets (same company)

After time from the heating and cooling cycles these exhaust manifolds warp and very easy blow across the gasket. You can have them milled to a certain point but I also found using a thicker gasket can help if somewhat more material is milled.

Thanks. I think my issue was that I had some spots on the flange that was down to the metal, while the rest was still powder coat. Then I had them painted. So this created low spots - that powder coat is thick. So I was able to take an angle grinder with a fine grit flap wheel and gradually remove all the paint and powder coat along the flange until I could just barely see the metal starting to show through. Then I took a block and sand paper to finish it off by hand. I used a straight edge before and after and it came out great. I just had to knock off that thick powder coat since some spots along the flange did not have it. I will just spray some high temp heat paint on the flange now and I should be good to go.