Personally I would not use RTV. Especially if you are using the new metal and silicone Fel-Pro gasket set as I did.
My pitting wasn't that bad (the worst part is no deeper than the head of a pin), but here's how I did it...
Go to your local autoparts place and pick up some fresh JB Weld. (I opted for the standard gray version, not the 4 min quick dry black stuff... and don't ask me why.) And some 400 grit wet/dry sandpaper. (About 6-8 sheets.) Scrape as much of the gasket material off as you can using a good quality gasket scraper. Dab some gasket remover on to the surface, and use straight pins to dig out the remaining gasket material (or whatever) that's stuck in the pits. Dab some more gasket remover on and use a small (clean) brass brush to get the rest of the junk out. (You may be surprised just how deep the pits really are.) Once you're sure no gasket material is left in the pits, prep the area with acetone or alcohol using a clean toothbrush, then wipe dry.
Mix up some JB Weld on a paper plate and use the corner of a razor blade to fill in just the pits. (You need to push it into every nook and cranny.) Then take the same razor blade and smooth out a thin coating over the entire pitted area. Try not to make the whole thing any thicker than 2 or 3 sheets of paper, you don't want to kill yourself sanding it off. I had very little pitting on the heads, so I just used a VERY thin skim coat on those areas. That also reduced the amount of epoxy dust that I needed to keep out of the engine.
Now here's the hard part, let it cure! - I let mine cure for about 48 hours. When you pick up the paper plate and bend the left over epoxy, it should snap like hard candy. When it does, the manifold's ready to sand.
I then wraped the 400 grit sandpaper around a 3" by 3" slab of perfectly flat milled steel. Some people like to use plate glass. Sand the area using only the 400 grit sandpaper. It's not as bad as it sounds, I think all four water ports on the manifold took me less than an hour. When the sandpaper clogs, just use a fresh area.
If you left the injectors in the manifold, you may want to cover those open ports with tape to keep the dust out. And use the sandpaper dry, not wet. When the epoxy looks like it's becoming invisible (you can see the pit marks through it) your pretty much done. I took mine down to the point where the only epoxy on the manifold was between the milling marks. (And in the pits of course.) You should end up with a continuous, hard, smooth-as-glass finish. You must not be able to feel where the JB Weld stops, and the aluminium begins.
That's about it. But note... everybody I know does it a little differently, but this is what worked for me.
