i say do what you want. it's your truck and you paid for it with your money. if you want to swap the drivetrain into something else, go for it. i do think you'd be better off with a v8 in the wagon simply due to the weight of it, but if a v6 is your gig, do it.
there will always be someone willing to buy a shell and transplant another motor into it. whether or not you'll get prime dollar for it or not is another thing all together.
i think a 67 chevy ii wagon with a syty drivetrain in it would be sweet. i know hood put one in his deuce, but it wasn't a wagon. if people were really opposed to you removing the drivetrain, i say pony up and buy the truck off of him. otherwise, stop bitching and moaning about what he's doing with *HIS* truck.