If you have been working on the car without charging the battery, you most likely drained it. I bet you did not burn the motor, just not enough power to it.

 

I charged the battery and rechecked the ground and the motor works. However the top is still not moving. Again, I run the top motor for a while and then the fluid stops moving. Could this be an electrical issue and draining the battery because the car is not running?

 

Some. The battery is 12V, while the alternator should be providing 14V with the engine running. Running the top motor with the engine off is normal, though, it should work fine that way.