Edit: The problem on this first video is fixed. You can possible see/hear the hand motor running during the issue on the first video. Scroll down and now view the video of the pin turning on but the hand not working properly. Please chime in with some advice and hopefully a fix.
This is second issue is now fixed but both upper flipper buttons are not registering. They show 'open' on the single switch test. Everything is seems to be working. I wonder if it is possible that I fried something else on the MPU when I shorted stuff. That, or maybe a fuse though I don't find a fuse singularly responsible for those switches. Again any and all help is appreciated.
SOLVED: see below. I edited the title of the thread to hopefully help someone in the future with similar issues.
Thanks!