I think I've used all three, Fel-Pro, Mahle, and Victor Reinz with good results. On the valve cover gasket, make sure that you get the one without the bolt holes around the edge. The instructions say to fill the holes with RTV, but that's a kludge, IMO. Yes, there should be rubber seals under the bolt heads. Definitely use RTV on the head for the valve cover gasket. I doubt the extra 1/16" makes a difference unless your two studs are too long to snug up the cover against the gasket (valve cover itself distorted.)

On the side cover, clean everything off well and use RTV on both sides of the gasket so that sucker is sealed up well.

Kevin
1951 Chevy 3100 work truck
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1929 Ford pickup restored from the ground up. | 1929 Ford Special Coupe (First car)
Busting rust since the mid-60's
If you're smart enough to take it apart, you darn well better be smart enough to put it back together.