You could relocate the Alt, by removing the A/C compressor, and putting the alt in it's place. You would have to make a bracket. I think there are some on here that have done this.
Having some sort of water sprayer with you to clean out the alt, and a hammer to tap out the dry stuff. If your doing a lot of mud, and dding the XJ, then carry an extra alt, and a battery jump box, or a second battery.
I would seriously consider a snorkel. Even a home-made job. Some have relocated their intake into the fire-walls fresh air intake. You wouldn't even see the snorkel, and then you would have some protection.
Put some pool noodles in the doors if you take the plastic liners out of the front fenders. will keep mud out of the door hinges.
Take the carpet out, and use some sort of painted liner. Or cut the carpet so you have the front section to protect your legs from the floor board heat. Then if the carpet gets dirty, just pull it out and wash it.
Change you fluids after every deep water, and or mud crossing.
Make sure you have good solid tow points on the Jeep. A winch would be nice to have as well. If you go winch route, keep it covered or get a winch cradle and use temporary mounts front and rear for it. Then strap it tightly to the inside of the Jeep where it's clean and dry... and it won't bounce up and knock you in the head.
xtend diff breathers inside of the jeep.
TSL's, boggers, or some sort of tire that will clean out well. Some sort of way to air up and down your tires.
remove excess wait... if you don't need the rear seats, take them out, etc.