I am currently converting/building a 46 3/4 ton flat bed to a 46 1/2 ton short bed. I am using a S- 10 frame and suspension.

I think you are asking about aligning the cab, bed, and running boards to where they are in a straight line.
If your not using the original frame, you first must get the cab to where it has to sit in relationship to the radiator support. The distance from the radiator support to the cab is critical. (The front fenders connect the radiator support to the cab and running boards)
then I would start by getting the running boards level with the ground by using a bubble level. Once you get the radiator support, cab and running boards connected together, you can secure the running boards to the frame. Then set the bed on the frame and check the gap between the cab and bed to make sure it's an equal gap from top to bottom. Adjust the bed to get the cab to bed gap equal and then raise or lower the bed to close the gap to the splash panels between the bed and running boards.

Adjust the bed back to front so that the running boards connect with the front fenders and the rear fenders.

It's going to take a lot of trial fitting to get everything lined up right.

I hope that helps with what you are triing to do.

Frank