It wouldn't hurt to file across the intake runners as well. Same process. You will be able to see the uneven surfaces pretty quickly by the shiny metal. You won't have to do near as much on the aluminum. Just go slow and be deliberate, and you HAVE to go across two or more runners at a time to keep it even between the runners.
Personally, I don't like sealants on the manifold sealing surfaces. Flat mating surfaces, a good gasket, and proper torquing should take care of any issues. My aftermarket Clifford intake does not seal the same as my stock intake. It is much more difficult to eliminate vacuum leaks. A primary cause is that the Belville washers do not sit flat on the runner ears.
Go Fish! <*////><
But the right word at the right time... "Hey, give me a little hug!" That's the difference between lightning and a harmless lightning bug!