You had the valve cover off ,you might have simply miss located the bowden cable location .The bowden cable joint and the cruise control conrod joint are within an inch apart and are commonly misplaced especially if the cruise control has been deactivated (all its conrods removed)The slack, or lack of plays a big part in the engine and trannie recognizing each other.I had the same happen after doing a valve adjustment ,recheck the bowden cable .