Are you sure the 2008 had the same GCWR ? In 2008 Ford increased the GCWR by 2,000#. That 2007 E450 when it left Ford, had a 14,050# GVWR and a 20,000# GCWR. After Tioga stretched the frame and put their house on it, they downgraded that GCWR figure. In 2008 Ford changed the specs to 14,500# and 22,000# respectively. So Tioga upgraded the GCWR somewhat, but it's still considerably less than what it was when it left Ford. It's only in the last year or so that SOME manufacturers are rating them at the full Ford rating.
If you have a 3,500# rated hitch, you definitely want to upgrade that to probably a 7,500# hitch or so, and have a qualified hitch builder/installer check out the frame extension and reinforce it if necessary. Another issue would be tongue weight. With a 4,500# boat if you can keep the tongue weight around 7% (315#) or so, it should be sufficient tongue weight to trailer properly and not be excessive tongue weight.