You didn't say one way or the other if you also got taller tires with the lift.. (I can't imagine anyone getting a 6" lift and not also getting taller tires)
If you did, did you also get new axle gearing to compensate for the taller tires? Taller tires will affect your final drive ratio and basically bog your engine down if you didn't change gears.
Not sure what you are trying to justify here? You already weighed your rig with the lift and all, and you came up with your actual payload left.. #500.
That does sound about right for what you have done.
Only you can determine what ratings you want to go with..
I've towed over GVWR on trucks before and the world did not end.. :)
But, that was my choice and it's what I did. But, that's just it.. It was my choice.
Good luck!
Mitch