On my 2001 800XL, the tops of the carbs and choke plates are wide open and visible which it looks like would make it really easy to splash water into them if there is any water in the hull. Am I missing some sort of cover for the carbs?
Here's what I found on eBay. item # 401551905419. $23.94, free shipping. Redline motorsports. It looks like it may be missing the flame arrester screen and mount bolts. If you contact him, he may be able to add them. If not, it's still available from "Babbittsonline" as for bolts. there 6mm you just need to figure length, and I'd use stainless if you can. Plus you'll need new seals for it. They are actually just a set of O rings.
Hope this helps.
The easiest way I've found to find parts for these old beasts. Is to look up the factory part # on Babbittsonline. Then serch it on eBay as "Yamaha" then add part # and then sometimes the description. In your case I serched. "Yamaha 66E-14480-19-00 air box"