The arduino is capable of producing the pulse sequences you need but without more info we cannot be sure what sequence the pulses need producing in, the current is being drawn by the motor and what other components will/may be needed.
The motor is enclosed so if there is a switch being tripped I can not see it. I was hoping to do away with the boards (MD3110 and A29L040L) and replace them with the Arduino to run the motor. Does that seem possible? I don't think the motor draws many amp's.
Maybe I can ditch the whole rig and replace the motor with a parallax servo. Now the big thing is getting it to count to 6000