Actually, everything is negotiable. Some dealers will say "shipping and set up not negotiable." Well, if you hear that it is time to go to another dealer, or get them to mark down the price of the bike enough to negate the "fees".
When I bought my bike we didn't even discuss set-up or anything. It was all "out the door" price.
There are services that offer information on dealer markup for a fee. It's like 10-20 bucks, but it is very good information to have. I don't know the site specifically, but I'm sure Google will turn something up.