Some of the connectors are more important than others, I use a clear plastic bag (both ends open) a wad of plumbers puddly around the ends and twist ties (or cable ties) on mine. It really is a toss up whether the sealing is going to be a hundred percent or not, your likely to want to get back into the connectors periodically to deal with oxidation or moisture.
Deflecting the mud or muddy water away from the motor is a good idea. Clean water really doesn't conduct well, the dirtier it is the better it conducts. Built up mud holds moisture and can accelerate oxidation. Muddy water in the alternator can build up a coating on the slip rings, between the brushes and slip rings causing failure. Same for the starter.
Running a vent from the distributor to the snorkel may not be a good idea, as the vent will cause negative pressure inside the distributor, which may suck moisture. careful use of RTV can get a pretty good seal on the distributor, but remember you'll 'eventually want to get back in there again. Using as little RTV as possible can make cleanup easier.
Mud gets in the radiator, dries quickly and will effectually cause some blockage. After it dries it gets harder to wash out.
The mechanical fan bogs your motor down when you get in deep enough, if it picks up mud it will really trash your motor bay and can damage the radiator.
Much of it is trial and error, I#ve developed a system over the years to check the likely trouble spots and periodically deoxidize and dry out the connectors.
Electrical line leak can also cause problems, 12-14 volts will leak to ground somewhat, if it leaks down enough to cuat more than a 4-5 volt loss, ignition and other sub systems can become weak.
If you have a stick you'll have to figure out a way to clean the clutch. It#s doubtful the water will be totally clean, the layers of dried mud build up and cause slippage.
A carry an extra alternator and *starter*, you almost have to clean them out after every diving expedition.
The longer it's underwater the likelier you are to have seepage, and from experience complete sealing is almost impossible.
I try to set up my XJ to be as maintainance friendly as possible, just in case a seal leaks someplace.