I didn't read the whole thread, pretty much just the first post.
If you are receiving that message, my guess would be that your break out board uses optocouplers and it has burned up, making it act as normally open switch now, instead of normally closed, triggering the software that a limit has been switched. Simply replacing the chip should solve the problem.
Those motors you are driving may be too big for your application. Bigger doesn't mean better. This is covered over and over again on thousands of threads over at CNCzone.com. There are people who are getting better results with their nema 23 motors, then with their 960oz. nema 34 motors. It's just how there inductance and voltage rating are.
Give Ahren a call over at CNCrouterparts.com. He's a pretty cool guy and very helpful. I bout 5 times NEMA 34 motors from him to use on my machine. I am building a very big machine, 4x8 but the gantry is built differently and more then usual weight to it, so I'll be using a nema 34 motor to control that axis and the z axis as well. Ahren can set you on the right track.
In either case, for safety reasons, you want to make sure you use normally closed switches, and place them in series. That way, if one is triggered (causing it to become an open circuit), it triggers the software. If the switch is accidentally cut or disconnects, it triggers the software, as the software will see it as normally open then, and shut the machine down.