Regarding your Z endstop, it seems that the microswitch has been bent out of position by the endstop screw on the bed platform.
The original mounting bracket is correct, but the switch itself is supposed to be flush with the PCB, see: https://drive.google.com/open?id=0B4QI9opJS9SbTUp3VE0tWHVSY1k
The first thing I'd do if I were you is to verify that the platform moves in the correct direction, pressing Z +0.1mm in the UI is supposed to move the build plate DOWN. If it doesn't, you need to change the Z motor direction in your config.g then try again.
If that works, I would suggest you take a copy of my homez.g and verify manually that it works as it should.
What I mean by manually is that you
- move the build plate down from the UI to something like 100mm (do this in small steps in case your steps/mm is incorrect, simply clicking "Z +100mm" might translate to some ridiculous value in those cases)
- click "Home Z" in the web ui
- verify that the build plate starts moving towards the hotend and
- use your finger to push the Z endstop to verify that the build plate stops. If it doesn't, hit the emergency stop in the UI before the bed crashes into the head/endstop.
E: I'm using the default 2 Z-motor setup, but it's a pain in the butt. Be glad you only have one, my Z axis gets all wonky as soon as I turn off the Z motors since one side will start sagging while the other will stay put. Probably the first upgrade I'll do is either a 1 Z-screw or 3 Z-screw modification. I kinda like the linear rod setup you have on yours, will consider something similar.