You can spray WD40 on the shaft to help inhibit any further rust issues, although there are, in my opinion, better products on the market that are specific to inhibiting rust. The boot will fully detach from the final drive unit to facilitate cleaning and re-greasing. Without a photo, I'm not sure what "gunk on the bottom of the drain plug" means, but if you're referring to the fuzz normally found on the final drive drain plug, yes, just wipe that away. If it's smooth in consistency, it's normal. If there is any grittiness to it, that is not normal and further inspection of the final drive would be in order. That is very rare though. Good catch. Now clean up the little rust that is there, apply some moly grease to the splines and some lithium grease to the both ends of the gator and put it all back together for an enjoyable season of riding!