So I'll keep the updates coming in case anyone is interested...maybe I'll inadvertently share some tidbit of knowledge that's useful to somebody.
Today I drained the fuel tank. It was WAY easier than I thought, aided by a siphon that I had purchased at Bass Pro last year for emergencies. Well it paid off big time. I used it to help drain the previously mentioned jet ski and get it afloat and now it made fast work out of draining 12 gallons of saltwater from my fuel tank.
It's the "self priming" kind that you shake a little to get it started. Very similar, if not exactly like the copper 3.5 gpm model here:
http://www.simplesiphon.com/products/
There was about a half gallon left that I couldn't get with the siphon, so I simply used the prime bulb to shoot the remaining water into a gas can. It didn't even have a faint smell of gas to it.
Next step with the fuel system: Change the water separator filter and add a half gallon of fresh, heavily oiled gas to the tank and run that through the prime bulb again. That should clean out the remaining pint or so of water and lube the pickup tube pretty well. I'll burn that slightly watery gas through my weedwacker.
When the rest of the electrical items are taken care of, and I'm ready to get her in the water again, I'll refill the fuel tank completely with a little extra oil and some Startron to burn through. Again, the motor itself wasn't submerged so once the fuel tank, lines, and prime bulb are clean I should be ok there.
Any other suggestions on bringing the fuel system back up to speed?