I would think that $6k is a little steep considering you can get a used '03 for around $6500. With all the new liter bikes coming out this year, there will be a glut of nice 600's from people chasing the latest and greatest.
Modifications don't really contribute to the value of the bike. If they happen to be something you like, great... but a majority of that stuff is very personal.
Used helmets are just bad news. First of all, it has to fit you. Second, if the thing has been dropped or abused you may not be able to tell just by looking at it. You will want to take the liner out and look for small cracks in the painted foam. Even than, I would not trust a used helmet without sending it back to the manufacturer to be inspected.