Rich:
I have not ever done this conversion, but base this following information strictly on measurements we have taken from trucks. Hopefully, another board member that has done this conversion can provide their input to your problem, based on their personal experience.
For the 54 bed, the cross sills are at 2-1/2", 26-11/16" and 53-11/16" measured back from the front bed panel or the front edge of the wood, and there should be an angle strip bolt hole at each of those locations. There should be a bed to frame bolt hole in the frame at the 53-11/16 cross sill. The bed does not have a bolt to the frame through the 26-11/16 cross sill. The 2-1/2 cross sill will not quite line up with the original 49 frame bolt hole, so it may have to be drilled in the frame to line up. You can't move a cross sill without changing the bolt holes in the angle strip which is what locates the cross sills in the bed. If you decide to move a cross sill from the original 54 location, then the bed strips will have to made with a custom hole pattern, which is easy enough to do if you want.
The measurement from the bottom of the wood to the top of the frame is 4" where there is a bed to frame bolt. That is where you will have to block the bed up to get the correct clearance. Your bed will sit a couple inches higher than a stock 54 truck because the 54 frame did not kick up so much over the axle as the 49 frame. Splash aprons may have to be custom made to adapt the different height. You will probably have to make custom wood blocks to get the 4" height right.
Hope this helps.
Mar-Ktech
