You can check for shorts to the motor case by measuring between the armature posts and the case, and the field posts and the case. You may have some amount of resistance due to dirt, carbon dust, etc, but you shouldn't see a dead short (with all cables disconnected).
While the cables are disconnected, check for continuity between A1 and A2, and also between S1 and S2 to see if something has come loose inside. Sometimes its just a matter of moving brush leads inside the motor a bit to eliminate a short.
If these checks are OK, you can test the motor operation using a coule of jumper cables by connecting 12 to 24 volts (part of the pack - just a couple of batteries) where the B+ and controller M- connect to the motor (S2 and A2 on your setup). This will turn the motor enough to show it works, but won't overspeed the motor as long as you use low voltage. Make sure the cable is also connected between S1 and A1 to complete the 'series'.
Here is an example video I made a while back -
Make sure the trans is in neutral, or jack the rear end off the ground to be safe.
As far as the batteries go, use your regular battery charger and give them 30 minutes on charge once a week - but don't boil the water out of them.