First off welcome, cnc is an intersting place between the realms of mechincs and electronics. Your questions are none that have not been answered before I suggest in the future before you ask them that you use the forum search functions as there many areas to cover. But I will answer them to the best of my knowledge and what you are planning on doing.
1. The control has no way to know if the stepper has not completed a move, you answered the question yourself its "open loop". This is the biggest difference between servos and steppers, on most low cost low power systems such as taigs and sherlines steppers are more then sufficent. The stepper control has no way to know if the lead screws broke either so you are reading into the issue more then needed I think. This other then the intial setup is not a normal worry if you run the machine in its normal parameters.
2. This depends upon what kind of control, interface board, and software you are using. Some setups the the limits and home switchs are not even needed but you should IMHO have them for saftey reasons. The software will almost always stop you from exceeding the limits of the table. The wiring could be done directly to the control board in a couple cases but most often the wiring is attached to a break out board. You may wire a limit switch to the control board in such a way that it shuts it down if the "hard limit" is exceeded.
3. The control software takes care of the lead on you machine, in can be fine tunned with measuring insturments while setting up. The motor control strictly controls the motor and depends upon the software to preform its task. The thickness of the lead(or axis) does not effect the movement only the teeth per inch/mm.
You may want to vist artsoft they make Mach 2/3 series of cnc control software and are excepted as one of the leaders in the homeshop area. They have alot information on there product and cnc in general in there instructions.