3" and 4" Schedule 40 pipe ODs are 3.500 and 4.500 respectively. Add at least 1/16" for the hole saw.
You may have trouble holding the drill for a self feeding bit in the size you are looking at for 3 and 4" pipe.
The solution for the double plates is usually to clear the hole saw after each plate. If the wood gets stuck and stays in the hole instead of coming out with the hole saw, you may need to apply a chisel or put a screw in the piece to pull it out.
I have found that a Roto-Zip with a 1/4" straight carbide bit does a great job where you may not have exactly the right size, or where you may not have clearance for drill access. Just handle it like a big Dremel tool, but with both hands. And hang on tight. I had one come out of my hands once and it fell and tore my pants where it came within a couple of inches of affecting my social life.