I too had to make that decision when buying mine 5 years ago. Since I haul a boat on 95% of my trips I liked the 990 better since it allowed a shorter hitch extension. Plus, when on the inside it felt to me that the added length didn't make the camper feel much bigger. What do you gain, a coat closet or something like that (remember I am comparing 2007 models). That minimal closet/cabinet space was not enough to override my engineering mind looking at the shorter hitch extension.
4000lbs in the bed? I have yet to weigh mine but don't most of the posts on here say they are closer to 5k when loaded up and ready to dry camp with water and everything?
What year 3500 you looking at? If you are worried about following the payload rating exactly and never going over it the Chevy had the lowest GVWR for the 2000 era trucks I was looking at. Newer trucks have increased. Heck, my 01 dually F350 GVWR is 11,000 while my father in laws 2011 SRW F350 is 11,000ish lbs.
Good luck with whatever you buy. John