haaha , That's funny you post this now! Certainly what you say is true and I found out the hard way after crossing with the ferry! Indeed only 90 days is given at the ferry but I understand that all the road ports will give 1 year (from Brazil also).
If someone is looking to store their moto in Uru, Kevin Lemes is the fellow to help with that. (firstname.lastname@example.org) . Kevin lives in Montevideo and is a real nice guy. If you need any work done on the bike his father has a great shop with a few mechanics (also real nice people) and they will help out.
My KLR is nestled in there right now waiting to be ridden home in a year.