Dave, I was dreaming about his last night and here's what I came up with.
I would take the 3" cap and drill some very small holes in the bottom, then drill them around the sides so when they stack the whey drips out the bottom of the top mold it doesn't have to pass through the curds of the other cheese to get out, it can just sit on the follower of the bottom one and drain out the sides.
Next I would take just a regular 2 1/2 PVC pipe and cut it into 3" high pieces and notch out the bottom, so whey can escape. Make sure you cut the PVC with a pipe cutter for copper so it will be square. Next sit the PVC pipe on a level surface and put the cap on top (cap upside down of course) and use a small torpedo level to level out the cap, then hot glue the PVC to it. You could use drinking water safe PVC glue but it won't give you enough work time to level it out, you know, it sticks almost instantly.
There you have it. The base and mold are together and can stack easily. Besides PVC pipe is a hellofalot cheaper than couplings.