Alternator swap problem???
 

After doing the alternator swap, when I plug the two wire clip into the alt and touch the red wire from the passenger fender to the battery, there is a tiny spark. When the clip is not in the alt. there is no spark. I unplugged the harness from the firewall and undid all the lights and it only sparks when the two wire clip is joined into the alt. Does this mean my alt is using up battery?

If your alternator is generating a field after a while it will get very hot too the touch if it's not spinning.