#1. yes, i agree, unless you are very skilled and have a lot of experience with that particular engine and the particular sort of modifications and goals you're looking for, don't touch the ports.

#2. that said, port matching is not a big deal, as long as they are not really far off in the first place. if they are, you should probably start by drilling out the holes, as described, and trying to get it aligned better, as that is more likely the problem. if they are far off, i would try getting them a little closer, but i would never take off more than 1-2mm of material, and you would have to blend it into the runner well, which goes back to #1. so if it's not very close to perfect, don't bother, or don't do much. maybe just round off the edge that is interfering with flow a little.

#3. port matching to the gasket is probably useless, since the gasket may or may not sit so perfectly straight on the head, anyways. you should be trying to match the manifold to the head, then the gasket as well. i just can't see matching IM to gasket helping much. might even hurt if gasket doesn't fit head well (and of course, the gasket has a little bit of a loose fit to the head as well).