When selling modified cars, I was always told to take 1/2 to 1/3 the value of the add on parts AWAY from what the KBB value of the car is. Keep in mind, this is stuff like cams and heads and high end "invisible" stuff like gears harnesses and chassis items. I doubt wheels and rims and a lift would effect the price too much one way or the other as long as the buyer felt they wouldn't need new ones in less than a year.
I'd agree that you would get more for your winch, dual battery setup, tuner, LED bar, etc... if you parted it out. I'd be running away from a bed lined tub, unless I knew you and your work. Tire carrier, Jerry cans and hard top would be worth more sold separately as well. Just my 2 cents - every market is different.