Same thing here. PO had put sheet metal over the wood and i didn't want to mess with it. You can get it off, but putting it back on is another story.
I had to take a cutoff wheel and cut some of the bolts off mine, but it wasnt' that hard. I am re-doing the bed any way, so in the end I will deal with new bolts...
See my photo link, there is a pictue album in there that shows the bed puller I made, from a pattern I saw on a body supply shop on the internet. It is for a fleetside, and may not work for a stepside, but for what-its-worth. Good luck.