So, would it be worth it to keep these tires/ wheels and cut out the fenders and possibly do a 3" body lift to my truck, or should I just sell them and get a smaller tire package?

I think your answer is contained in several of the above posts.

There is not much you can do to fix the rubbing. Fender is some of the problem, frame is the rest. Overall, these tires are not a very good choice for your rig. Especially if the rims are the size you think they are. Eventually, the rubbing will probably destroy the tires and then you will essentially have no tire and no money.

Good Luck,
Michael