Before you get into cutting a new gasket, or gluing the ones you have, tighten on the timing cover with the intermediate gear in place, and measure the end play. There is a measurement range for this in the build manual. This will tell you if cutting the ignition side gasket out of thinner material is likely to give you a problem or not. That's the one to replace if you're going to cut your own - as you say, you need to keep the exhaust side gasket with the silicone for the water log.
Permatex Aviation 2H is the stuff the guys are referring to if you can locate it.
Let me know if you need the end play measurement range and I can pull it out of the manual. It's not too likely that you'll have a wrong end play with the gaskets in place.
Re the oil pump drive gear, I don't know what manual you're working from, but have a very good look at the description of how this drive gear needs to be retarded (or advanced? can't remember right now) while installing your timing cover, with oil pump already in place but only tentatively tighened. Doing this right will orient the distributor to the "right" place rather than in some random direction.
A separate point, related your mcmaster carr order: at least I've had issues with the timing cover, water pump, and the sump loosening after some time running. (No, it's not just a question of not tightening enough, I think it's from gaskets compressing over a number of heat cycles.) I would suggest you look into self-locking nuts, or double-nutting things, and checking the tightness after 500 miles or whatever.
Alcala de Henares, Spain