Yes you need to have the bunks stepped to support the hull per the manual that comes with the fountain. You are correct in that you can simply add the proper height and carpet to the rear of your existing bunks and then make you some solid ones. You also want the bunks to extend about 3" past the transom to prevent a hook or damage.
Also, might have to have a "cow catcher" v block stop below the winch line. The beak can play havoc with a typical winch set up. But you ought to be able to get it home with out the cow catcher. I'll try post a pick of my setup that I got to work very well.