1. I would check to distance from the Z axis sensor to the metal tab that trips it, ideally this would be closer than 3mm, I think mine are around 1.5-2mm. Otherwise it may be in the connections or wiring??
2 and 3, I have had my machine freeze on me a couple of times when stopping a file. I had to turn the machine off and on again to get it to work. If you have used any other CNC machines then you will realize that they all have their own bugs in the software. I wouldn't say these ones are too major. In saying that I still intend to chnage to Mach3