I have just mocked up my 46 gmc and this is what I finially came up with. First chalk a center line of chassis on floor, and two more lines parallel to the center line wider then the body, to use as reference.
1. Mount cab to frame square and with proper spacers shim where needed
2. Mount rad support and hood, moving rad support to get proper hood to cab alignment.
3. Mount front fenders, splash apron,and fender grill inserts ,to get proper alignment to hood and cab. Keeping fenders the same left to right on the cab
4. Mount box and box to running board splash aprons loosely on frame
5. Mount running boards to front fenders and running board braces loosely
6. Mount rear fenders to box and running board loosely
7. With fenders attached to the running boards you should be able to place the box in it,s proper location.

I used fiberglass fenders and running boards and spent about 30 hours to mocked the complete body to frame.
Hope this might help
George