Is it possible to do something about the poor placement of the alternator on the X? Would buying an aftermarket one with an external
regulator provide protection from water and mud be worth it or is it just another part waiting to fail? Other than staying out of water and mud, what can be done to help? Sorry if this is common knowledge and I just haven't been told.

Thanks in advance for you help.

Everyone doesn't like where the alternator is!!! People are working on solutions though. Problem is you have to fab some new brackets to place it high and the A/C unit down low. Making brackets and longer hoses for the A/C unit too! Just try not to go in water deeper then the center of your wheel and you should be okay! That is my rule!