This is my take on an x-rod mount, inspired by the Prusa Mendel. It presses a screw directly against the rod to clamp it in place, and is extremely low-profile. I had trouble printing twotimes' version (the y-axis kept skipping when transitioning from the base to the clamp), so I built the clamp into the base.
Press the captive nut into the slot above the rod hole (tighten it onto a screw to press-fit it and make sure it's aligned), then insert the rod. Mount the clamp to the inside of the Cupcake body with four screws, then tighten down the clamping screw to lock the rod in place. You'll probably need a ball-end hex driver for this (my Makerbot came with one).