is there any way to waterproof an alternator? or make it more water resistant? i know from experience that when you lose current from the alternator, you also lose power. has anyone ever attempted to do it to theirs?

 

There was an options somewhere that was a rubber "boot" that went over the Toyota alternator that at least makes it "mud" resistant....

 

The problem with protecting alternators from the elements is that they are air cooled. Most anything you do to keep stuff out will also hinder airflow and can cause it to overheat and possibly catch fire, or at least burn out before it should.
You might be able to fab some sort of shield around the alternator which doesn't affect airflow. Or maybe shellac over some of the exposed wiring, possibly improve the protection on the regulator, etc., but the contacts / brushes will have to be free of anything and that can still cause failure when wet- doesn't take much to short out 70+ volts AC.