Stick dielectric grease on all the connectors. Don't forget the spark plug boots. Spray some silicone lube on the back of the harness where it comes out of the cab. Seal the dipstick tube to both the engine and transmission (if automatic, of course). Move all breather tubes to hood level including the ones for the transfer case and automatic transmission.
I regularly drive and park my truck in water that covers the starter. Periodically I drive in water close to 4' deep (waterpump deep is as deep as I want to go). After I get done submersing I just let the truck idle for about 15 minutes to "dry out" and the truck doesn't get shut off until I get back on pavement.
The starter shouldn't short out. It's series wound so unless you have a bad solenoid there is no way for it to short out. I recommend hosing out the starter and replacing the solenoid if you really think that's what your problem is.
Once you get past waterpump deep you have to start sealing everything like the distributor, PCV system, oil fill holes, power steering pump.... blah blah blah. Not to mention it becomes time to start worrying about waterproofing the interior.