tyhoppy, you bring up a very interesting point.
I do not know how one would "waterproof" an alternator. They do exist, I just do not know what exactly makes them water proof.
Then again, a mopar alternator has minimal electronics inside the case. The windings themselves are "waterproofed" with a clear lacquer to prevent shorting. The regulator is mounted remotely, so that is a plus. It seems to me, the only areas of concern, would be the diode bridge, the connections, and the brushes. Not much you can do for the brushes. I do suppose the 3 leads from windings to the bridge could be covered in some sort of silicone, although not standard rtv, since rtv may corrode connections.
Protecting the regulator is the easy part.
It is possible to make gaskets/silicone to protect the starter motor from water intrusion. This includes the solenoid.
It is also very feasible to use an external remote mount solenoid, so it may be mounted higher up away from water. This also prevents the starter cable from being live at all times, which is the way stock system is. (even when switch is off, the cable still has full battery power all the way down to starter)
An electric fan is a HUGE improvement over stock for this.