Never, ever use a sealer where intake manifold vacuum is applied to the gasket. If you can remove the mounting studs and draw-file the mounting flange smooth, no problem. Stuff a rag down the manifold to keep filings out of the engine. It might be possible to use J-B weld or some similar type of filler to smooth the gasket surface, but I'd prefer a smooth file-finished surface, or a replacement manifold. A vacuum leak there can be terribly frustrating with its effect on performance.
Jerry