Re: waterproofing ?\'s
Well, get rid of the mechanical fan first. Anything you do doesn't really matter until you quit flinging water around under the hood. Make sure you have your wheelhouse rubber flaps covering enough so when driving in the water your tires aren't splashing underhood.
Next, put dielectric grease on everything. You can get it from most electrical supply shops for the cheapest. Dielectric grease is not the same as anti-oxidant grease so don't buy that. Put it around the base of the cap as well. You may have vents and drains in the distributor cap and base so look for them. I don't recommend blocking them off but baffling them would be good. Make sure the coil is sealed still along with no cracks in the spark plug wires. If the wires are tired it is time to get new ones. Water just promotes spark jumping from the boot down the insulator to the metal. GM HEI people usually RTV the coil into the cap but you can't exactly do that.
Now that you've got the electrical and spray problem solved it's time to go after other engine related stuff. You have to track down all vacuum lines and make sure they are in working condition. If you happen to have a charcoal canister you should disconnect it from the PCV system and plug the lines on the canister and the line going to the gas tank. The throttle body/carburetor needs to be sealed if it doesn't vent into the air cleaner. The breather element for the PCV system must be taken care of. There is no easy solution for this because they tend to be pretty leaky. Don't forget to RTV the oil dipstick tube at the base.
The air cleaner system is an interesting issue. I don't worry about it because as long as water can't splash in I never plan on being in water that deep. Once you start getting into water deep enough to submerse the air cleaner you need a sealed distributor.
This will get you so you can operate it at waterpump height water. If you want to operate it any deeper you should've bought a submarine. Running it any deeper and you're asking for trouble with the distributor, sucking it in around the valve covers, through the crankcase breather, in the air cleaner through any one of the seams, et cetera. Not to mention at waterpump height you already have your pulleys flinging water all over the place under the hood.