Deve,
As shown on the assembled 3100 bed (on truck) I did the same as below. I use this folder to illustrate since my 3600 bed is different as far as number and frame attachments.
3600 Layout:
https://www.flickr.com/photos/advance-design_parts_co/8129083044/in/album-72157631867396207/3100 Layout:
https://www.flickr.com/photos/advance-design_parts_co/8130479975/in/album-72157631884205225/ As you trial fit the outside boards you can see where the bolt will go, mark it from underneath, drill a pilot hole smaller then the attachment bolt, check it (I used some long 1/4" bolts), if it is good that is the time to drill with the Forstner bit as it will not center on the final large bolt hole. Drill the Forstner hole to the same depth as the washer so it sits flush.
The final hole is larger then the bolt (5/8" I think, to allow for adjustment) once they are all marked/drilled you trial fit everything.
https://www.flickr.com/photos/advance-design_parts_co/8130475087/in/album-72157631884205225/The factory design allows the final tightening sequence to adjust with the offset washers. It has been a while since I did mine but it is measure twice drill once kind of exercise, thus the small pilot holes. That is a key because with anything larger than the starter point on the bottom of the Forstner it will wander and tear the wood up. I drilled trial holes in scrap wood before doing it on the actual oak I used so I was sure of the technique required. It is also worth noting on a 3100 bed the attachment boards have not only the sill holes but all of the bed rail to drill so it needs a bit of precision (and slight oversize on holes) to make it fit up correctly.
https://www.flickr.com/photos/advance-design_parts_co/8130499698/in/album-72157631884205225/These beds and attachments are designed (very clever) to allow the bed to shrink, grow, and respond to full load conditions.
