OK, I've figured out how to tell whether everything is aligned. Even if the primary chain slipped, there is no way the secondary chains would have slipped. Ergo, if the large camshafts slipped out of alignment, the small ones would be off as well. I'm assuming those are exhaust cams, or VVT cams? In any case, THOSE sprockets DO have marks on the rear timing cover. So as long as my copper primary chain matches up to its notch, and both secondary sprocket marks match up with their marks on the rear timing cover, everything should be all good.
I actually removed the new water pump. I have decided that removal of the bolt is priority number one. I was hoping the pump would go in its crevice a little better, but now I see how crucial that third bolt is - for installation as well as alignment. Removal was easier, but the pump and o-rings still got scratched up, as did the inside of the water pump crevice. I will be removing the burrs inside the crevice and maybe ordering a new pump.
At this point, the plan is to make a small punch mark and try to drill a hole in the bolt, then extract it. The bolt is sticking out a little bit, but not enough to file down and grab with a pair of channel locks.
EdBwoy gave good advice regarding moving the chain back and forth to slip the chain over - that, along with a couple of pry bars, helped to get the pump out. Getting the new pump in was not as difficult, but still required some prying.
This madness is

for all of you, I'm sure.