Your long bolts are 3/8 inch carriage bolts. You should have two that are 12" long. They go first thru a 1-1/4" diameter washer that has a square hole offset, then through the bed wood, the #1 cross sill (closest to the cab back) the wooden block, the rubber or neoprene pad and then thru both top and bottom sections of the vehicle frame.
The other four 6 x 3/8 inch bolts are for the #3 cross sill and the rear cross sill. For the #3 cross sill, use the same order: bolt thru the washer, bed board, cross sill, wooden block, pad, etc, but the bolt only extends thru the top side of the frame rail.
On the rear, you do not use wooden bed blocks, but you do use the neoprene pad. The rear cross sill has blocks or ears already welded onto the sill. Follow the same order: Bolt thru the washer, board, cross sill, pad and frame.
The #2 cross sill is not bolted to the frame. It is fastened only to the bed sides, boards the sill itself.
On the other bed bolts, you're right. The 5/16 ones pass thru the angle iron on the bed side, then thru the board, the sill, etc. The 1/4 inch go thru the metal strips, passing between bedboards. You should have seven holes in each metal strip. Some of these bolts will pass thru the sills...others will be between the sills. The larger (1-1/4") flat washers are used on the bolts that go thru the metal strips and pass between the boards but not the sill. They touch a board on each side underneath and you don't want to overtighten them and bend the m,etal strip. Where these bolts pas thru the sill, use the 1 inch flat washers. Of course, lock washers on every bolt before the nut.
