Two common problems are encountered after replacement of the motor control (MC) board in the NexStar 11. (To see why it might need replaced, read here.)
First, the scope may point south instead of north during the GPS Alignment routine or you will find the left arrow button moves the scope right while the right arrow button moves the scope left. Most likely the MC board you replaced was the oldest version and one of the cables you reconnected had a short extension cable harness that reverses the azimuth motor leads. Simply remove the extension harness and connect the cable directly.
Second, you may have problems ranging from no movement at all, to inoperative compass or GPS functions. Check to be sure all of the cables to the MC board are correctly oriented, all the silver pins on the board are in a corresponding hole in a cable connector, and all the connectors are fully seated.