A truck like that is worth only as much as the buyer is willing to pay. Where one fella might understand what you have into it and be more than willing to pay 3k, another might not give a crap and use the amateur paint job, age and wear as an excuse to say it's only worth 1500 to 2000. Also, alot of people see big tires and lift and automatically assume that it's been beat. Unfortunately, there are more hagglers and tire kickers than people who appreciate quality parts.
Even though you have a small fortune in the things you've done, your truck really only appeals to a small, specific group of people. That is, a person who wants a toy to go offroading with or maybe a truck to keep around the farm, etc. Especially with gas the way it is, your average buyer would not be interested in it as a work truck or daily driver.
I personally have modified several cars and trucks with loads of aftermarket parts and never once have even came close to recouping my "investment". So be prepared to take a hit, as much as you may not want to. If you were up to the work, you would probably make more money by selling the aftermarket stuff separately from the truck and going back to stock as much as possible.
I think it's a helluva truck for someone that really wants a tough, capable Comanche. That being said, I would list it as is for $3000.00 and see if you get any bites. If not, sell the tires and lift out from under it, ask $2000.00 and go from there.