That 3250 payload in the brochure for a stock F-250 is a XL with manual everything, 6.2L, Reg cab Long bed 2WD, 10k GVWR Package and the small fuel tank enough fuel to go 10 feet.
My CCLB with the Gasser has a payload rating of 2790 lbs.
I'm guessing you lost even more of your payload rating to your heavier engine and any extra interior options depending on your spec and GVWR. If you don't have the 10k GVWR package you lost even more payload rating to that.
Can you tell us the spec on your truck? Trim/options?