You are right, a spacer is needed under each cross sill mounting point. The rear sill has a taller mounting bracket and does not need a separate spacer. View a photo of the correct rear sill bracket on the Mar-K web site, it is part number 100717. If you do not add the spacers under the cross sills, the rear sill mounting will be taller than the other cross sills, and the bed will still not sit level. If you still have the original cross sills, the spacers can be cut off and welded to the new cross sills.

Mar-Ktech