I bought a 2003 for $4700 with 4700 miles in MI in October. Bone stock.
Goodies (especially at a dealership) mean nothing to add value to a vehicle. (Except if you see Ohlins forks, shock and Brembo brake systems etc...)
Even high end wheels mean nothing at this point.
That bike is worth no more than 5 grand period. Wear and tear is to be expected to a point. Scuffs and scrapes means the bike has been down at some point to me, that means, little unless you see frame damage. At some point in each of our riding careers, the or a bike has, will and will again go down if you keep riding. What is troublesome is the dealer did not fix this damage.(Within reason) Not to hide, but to show/sell a better product. The dealerships here would have fixed this type of damage, knowing it would depreciate their sales cost.
Now as for your extras: Make sure to ask for new tires if they are not in excellent shape. 2 year warranty (Mechanical and electrical), if you get 1 your good to go. (Probably won't use it anyway.) Have them pull the side covers off to check the wires, hoses ets... Check the tail section for alterations. If it has an undertail, check how the connections were make during the install. Twisting the wires and a good dose or 3M tape is not the correct way, sorry. LP connectors soldered and shrink wrapped is the best way I know. Then you add the electrical tape.
Ask for oil changes, fork oil change for sure. Have them show you the old fluid as proof they did it. (Just tell them you want to examine the fluid for yourself.)
Each panel that has scrapes or damage, ask for a cost to replace/fix this. Take that cost out of the sales price and see what the dealership says. (Be reasonable, point out only major damage.) Biggest thing is to be patient. Make a list of must haves and wants and check off the list as you talk business. It doesn't hurt to ask for more than you want then give the appearance you are making a concession...make them think you are sacrificing or giving something back. Negotiation part is what I like the most.
Mostly have fun at this point. There are many bikes out there and in this market with that bike, you are in the drivers seat.