Hmmm..... I see what you are saying. This weekend I will be doing a mock up of the bed box on the frame. I will look at it and see if there is any way I can discretely connect the rear sill to the frame rails.
I really like the way it looks without the stake pockets, but if all else fails I will put some new stake pockets from LMC back on.
I will check back in on Monday and let you know if I had any luck stabilizing the back of the bed.
Thanks again for the response.