I was in a similar situation a couple months back, ended up picking up an 08 with 400 miles that had more or less sat around garaged it's whole life. Since it's FI I wouldn't think twice, mines never even hiccuped. Also, paid 3900 for mine.
ya that is decent price there a slim market for used ones so if you want one your not exactly going to get the best deal because of supply an demand. I paid 2800 for mine but it does have 26,000 miles on it runs strong plus the guy had every recepit for oil changes with the miles on them so i felt comfortable buying it or i prob would have passed it up. my final thought was top ends fairly easy and not to expensive so i got out on the goodside i think. I highly suggest them if your commute is short or just to have fun on the weekends. I come from a motocross back ground and love mine. Rode it for 80 miles today lol my ass was hurting after that but its a great bike does everything well just not a rocket ship..
The wr's tank is plastic, I imagine you don't have to worry about rust too much. The oil has aged, it needs changed, the battery may be tired..etc. These are all things to expect when buying a bike that sat that much. It wouldn't be something that would worry me, but you may use it as a bargaining chip. My buddy just bought an 08 R model with 5k for $2900. I think 4 for an X with those miles is right on par. In the end It's worth what you feel you should pay. I'd do it.