I finally bought all the pieces and covered the underside of the new bed with epoxy primer and roll-on bed liner, hopping to prevent rusting out again. I started to loosen the upper bolts and I broke my torx bit. A friend thinks it would be easier to cut the heads off remove the bed and use a pipe wrench on the bolts after we get the bed off. I think if we cut the head off, remove the bed and cut the rear portion off the "U" shaped clip will the bolt fall or be forced through the frame or heat the nut/super cool the bolt . What's the best way too remove the bed bolts?

 

Even though my truck is not risted the bed bolts would not budge. Two of the bolts i cut from the top, used a four inch air cut off wheel and cut a X into the head and took the pieces out. The rest i used a cutting torch and five minutes to finish, two i used the cut off wheel were above the gas tank.
Now to answer your question once you cut the head of the bolt off , simply lift the bed up and off the truck. Then cut the u-clip where the bend is and the bolt will fall through the hole in the frame. The bolt is smaller than the hole in the frame

 

I use a 4 1/2" angle grinder with a zirconia flap wheel and grind the heads of the bolts off. I don't even try to loosen them anymore. You will see a outline of the shank of th ebolt once you ground down far enough on the head of the bolt. Hit the center of the bolt once you ground down far enough and the flange of the bolt head will pop off. Lift the bed off. Cut the captured nut clip and hammer the remainder of the bolt and nut out from the top and let the bolt/nut hit the ground. Dorman has a new bed bolt/nut kit, don't spend all the money on Motorcraft replacements.

 

Mig welded nuts to the tops of the torx bolts. I had to reuse mine and we cleared out autozone of all of their torx bits at 3 diff stores. Gotta love life time crap tools. I now have like 6 or 7 of them. Once you weld on the bolt they come right out with a impact or a big ratchet

 

Well broke a second bit socket and this time I started cutting the head of the bolt in a octagon shape and the rotten cross member vertically parallel to the frame. The cross member pulled up through the cut and rusted floor and the bolt fell though the hole in the frame. Worked for me, Thanks

 

Here's how i did it:

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