So I got to try out the new setup on my bike today. I don't know if it was the changes the guy at the shop made, or if I was just in a good mood, but it felt much faster. My cruising speed was higher and I could come out of intersections faster. And the handling felt tighter. Most importantly, while tomorrow morning is the moment of truth, my knees are feeling pretty good.
More specifically, the bottom of the pedal's circle has always been a bit of a dead spot in my stroke, and now it's not. So I think I even buy the hyperextension thing. Part of my wants to mess with my saddle height more, but I don't even know what I'm trying to feel. I think I need to lay down more mileage with the bike and see if I get a better idea. The biggest difference is probably the insoles, though, although the saddle height is a pretty major change too.