Try using an air chisel, those things work great for getting those rivets out.
I would take the bed completely off, makes things way easier, you've already done the hard part anyways by taking the bolts out of it, all you need to do it unplug the lights and take the three screws out of the gas filler neck.
I have a std. cab short bed also, and there was no interference with the cab mounts for me either, I take it only the ex. cabs have that problem.