I don't think that would be a good idea, extra head gaskets will give head clearance but won't help on the port timing. The top of the piston needs to travel to the bottom of the stroke to run corectly.
Using the same muffler from old motor.Are you using the same muffler from the old motor, or a new muffler?
After reading through what you have posted, have you cleaned up the intake? I like to remove all of the welding slag and smooth it as much as I can, I also cut the gasket out to the size of the flange after deburing it.
If the head gasket is blown (I assume this is the metal gasket at the top of the cylinder), wouldn't I be seeing oil residue leaking out from the gasket areas? It's perfectly clean as can be.Blown head gasket? Check your compression with a gauge.