Rich:
You should order for 54 model. The bolt locations for 54 are not quite the same as the 49 and the 54 is 1/4" longer. Strips length needs to fit the 54 bed length. Check that the angle strips on the bedsides are original 54 and do not have the front cross sill location shifted. If that 54 bed is sitting on the frame how you like it and has not been modified, then any adjustments have been made on the frame mounting pattern and height, not the bed. You don't need to order unpunched strips unless you think the bolt locations are neither 49 or 54 because of the modifications.

Don't forget your bed needs some kind of blocks under the mounting points of the cross sills and rear sill so the wood will clear the frame over the axle.

Mar-Ktech