Greetings: I encountered this problem 2 summers ago when I found a stepside box from a 2006 Ranger which I wanted to install on my 1997 B4000 fleetside due to rusted back fenders. I had been searching for a box replacement for years, not easy to come by. Here is what I discovered and the fix I employed. I was able to remove one of the two rear bolts using an impact wrench. There are 6 in total. I crawled under the truck previously and sprayed all the clip nuts with penetrating oil, I also soaked the heads in the bed and let the truck sit for a full day before starting work.
There was no way to even see the clip nut over the gas tank behind the cab. After removing the one rear bolt, I realized what I was up against; using an impact wrench on the other bolts would shear off the clip nuts and create an enormous headache. I talked to a few body shops, and some auto wreckers, they all told me they torched the bolts to remove the box, and in fact, the replacement box I purchased did not have any bolts. The Ford dealer informed me the original Torx bolts, and clip nuts were an obsolete part. Upon furthur investigation at the removed bolt, I discovered that when Ford built the truck bed, they welded a steel tube between the bed skin and the lower frame of the box. This was to carry the compression load from the bolt when they were tightened upon installation. AS A RESULT, you could spray penetrating oil on the clip nuts and the bolt heads until "the cows come home" with no effective results. The shank of the bolts were encased inside the steel tubes. and over years, that is where the rust accumulated, inside the steel tube. Here is what I did: I went to my local bolt supply house\parts store, and I bought 4 of their best quality 1/8 jobber drill bits. I came home and drilled a hole at about a 30 degree angle just off the edge of the big washer that was under the formed part of the head of the Torx bolt, I went through the washer, through the skin of the bed, and finally hit the shank of the bolt, which you could tell because the drill bit kicked off the shank, I used penetrating oil with a red nozzle and sprayed through the hole, attempting to fill the tube with fluid. Here is the reward!! by the time I did all 5 remaining bolts, I was able to remove all the bolts with a 1/2 drive flex handle and did not destroy any of the clip nuts holding the box to the frame of the truck. When I went back to my favorite body shop, the owner was flabbergasted at my sucess. I reused all 6 bolts and clip nuts to install my new stepside box on the B4000. Also FYI I used pieces of an old truck mud flap to install new rubber between my replacement box and the frame of the truck. However there is more to this story which I will post on another thread later, keeping in mind that MURPHY is always out there waiting to bite you in the ****. Courierlenny

 

Take a side grinder with a flap wheel and grind them off. I put a body lift on my old 1989 f150 before and had to do so.