Yea I just went with a girl to Ron Ayers and she bought an '09 for $4k OTD with an extended warranty and a helmet... I doubt a set of handlebars and some drill work to the muffler is gonna get you MSRP on a used bike. BTW I don't know where some of you are getting your numbers but the '09 lists for $3999 in the regular colors.
Oh and I can't resist but this is exactly what I've always talked about when it comes to first bikes... Someone lets their friends, a forum, etc browbeat them into a 250and they put 1000 miles on it before they get bored and want something bigger.
I mean that bike is barely broke in, has the oil even been changed yet?
IMHO you'd be better off trading it in to the dealer...I'd at least see what they'll give you on a new bike before you go through the hassle of selling it yourself.