More experiments. With the saddle clamped more firmly to the front way than it would ever normally be, using c-clamps carefully aligned over the top of the prismatic way, the back of the saddle floats .010 off the back way. With the front bottom clamping piece installed just finger tight so the saddle doesn't have vertical play but can still slide, the back makes slight contact on the left and floats .005 on the right. But because of the taper in the ways, the saddle can only move about half the length of the bed before it binds up. Also, the bottom surface of the saddle is above the bottom of the way, so the clamp is angled and not making solid contact with the bottom of the way. With c-clamps forcing the clamping piece into contact with the bottom of the way, there's about a .020 gap between the saddle and clamp. The feeler gauge drags a little more on the left, corresponding to the way being thinner toward the headstock.
I think I have to fix the taper in the ways. I'll do that first and see how everything else falls into place.