Wow, dude. That's intense. I just rewired my kinesis (no write up) and had the same problem as you: https://25.wf/images/rip.jpg. The solution isn't: throw away the circuit boards!! Just ignore it for the moment and when you're done, get a wire and solder between the two terminals of the broken lead. Just like what you did, but only fix the broken ones, not EVERY SINGLE CONNECTION!
Anyway, you're a brave soul, and the fact that you have a working keyboard now is a marvelous achievement! Great work!
The next problem I'm seeking to overcome is that I type with my hands under my desk: I converted my center drawer to a keyboard tray by removing the front of the drawer. As you mention, Kinesis Advantage is big. There is no room in the drawer for a mouse, so my mouse is on top of my desk. I don't use my mouse much, but it really is a pain to have to remove my hand from the keyboard and reach on top of the desk for the mouse. I have lived with this for a couple years, but I recently found a solution!: http://xahlee.info/kbd/iergo/kinesis_keyboard_trackball_by_hweller_2014-11-07-s1241x652.jpg
I haven't heard about QMK; interesting! I'll be sure to keep that bookmarked.
Regarding ripped leads, I think I had four or five. I was pretty careful pulling off the switches. I think I only had one ripped lead on the first hand well (I didn't know about it until I was done soldering the switches back on, then checked everything with a multimeter), but apparently got hasty on the second one, so I ripped several there.
I didn't glue the new switches into place. I think you said they're "friction fitted", but I'm pretty sure it's better than that. I think they have small clips, but I didn't look carefully. They seem pretty well in place, and now that they're soldered to these boards in the back, I can't imagine them coming loose at all.