I have a Mallory 4309 pressure regulator that I'm putting on a 90 RS with a carbed 350. It has 4 holes around the sides. Does it matter which one I use as the inlet and which one goes to the carb? I know that the bottom hole is for the return line to the tank and I assume that 2 of the side holes will have to be plugged. Also, can I put a fuel pressure gauge in one of the side holes, or does it have to go on the fuel line going to the carb?

You can use any one of the four side holes as an inlet.Use another one for the outlet and plug the other two.Bottom like you said is return line only.You can run a reducer fitting in either of the two unused ports to hook up a FP gauge if you want.I hook mine up inline right before the carb myself.