Don,
Yes, holding the stock firmly is the biggest problem. I tried all sorts of clamping arrangements but now I use dental plaster. Cheap, easy to use, sets in just a couple of minutes. I have a piece of 3/4 inch plywood that has a 3x3 hardwood block screwed to the back along the center of the long axis. The ply is about 8 inches wide by 15 inches long. When I get ready to mill the patch box recess, I tightly wrap the nearly finally shaped butt stock in heavy duty tin foil. The ply also has a center line drawn on it end to end the long way. I mix up a bowl of dental plaster and place a thick layer on the center of the board. I immediately place the stock in the plaster and adjust it so that the center line of the intended box recess lies parallel to the board center line. The plaster hardens in just a few minutes and exactly fits the contour of the stock. I usually screw down a wooden clamp block over the stock, through the plaster and into the plywood to hold everything tight while I mill the stock. (Obviously this clamp block is close to the area to be milled but not in the way of the cut.) I use the plywood part over and over, so it actually only takes a few minutes to get a stock ready for routing / milling. If necessary (and my eyeball alignment in the wet plaster was a little off) I shim the back side 3 x 3 clamp block on one end or the other in the mill vise until the centerline of the intended patch box recess is parallel to the mill table long axis. Once the milling is done, I knock the plaster off the plywood base and keep the base for the next mill job. I don't have one set up at the moment but will take a picture the next time I set up like this.