15 minutes later.... I can't believe how a millimeter can be the difference from it not moving at all, to being able to slide it in by hand. I ended up putting the piston on the old brake pad in the exact place it used to be, and then slid it into the caliper that way. Then I just used the orientation of the one I seated to align the other side. Worked like a charm. I used a bench vise and a crow bar to seat the piston rather than the C-clamp. The C-clamp was just too hard to get in that narrow space while being sure it went in straight. Thanks guys, this forum rocks!

edit: It seems like the boot should sit on the recessed part right under the lip of piston, but I can't imagine how it would stay there even if I could get it that low. I'm just putting the heat shield on, and having it push up against that. Sort of like Carpenterman was saying. I'll post back if this turns out badly.