If bypassing your board is alot of work then try disconecting your limit switches. one by one. Maybe one is giving you a false signal. Remember you were not using the 4th axis part of the board now you are.

now see thats a good idea. work smarter not harder. I will try these things and report back later in the week. right now Ive got a job to get done so im not gonaa be able to mess with it for a few days. any other suggestions before then will still be apreciated.