At the end of the day a truck is worth what you are willing to pay for it and nothing more. Additionally, paying a premium for a low volume vehicle still needs to be justifiable. I always take the NADA, KBB and Edmunds price for my area and average them together and that is my starting point. Additionally, for things that have to absolutely be there (like shocks, battery, tires, wipers and brakes) but are very often aftermarkets, I view them as pure neutral. The truck better have them. Just because you chose an expensive version, that is your problem; chances are I dont want that exact model that you chose and will change them anyway.
If you are buying it with some mods, keep in mind you are buying those used as well. Don't allow his labor to be figured into the price unless it was built for you to your spec. Here is a good article that highlights a similar point.
Selling a Modified Truck