Jimq: A B31 barrel is meant to use the 7 3/8 inch rod and a piston with a relatively high pin.
This is a B31 piston.
If you use the 6 15/32 inch rod you will need to make up about 0.9 inches based on the rod difference.
This is a BB32 GS piston and it has a lower pin but not enough to make up all the difference and it was made for a 6 7/8 inch rod. I do not know the height of a BB32 GS barrel.
I know you seem keen to run the short rod but it seems to be not all that easy. Maybe look at all the options. If you are using a later DB/DBD 32 GS piston you cannot use the 7 3/8 inch rod. The long rod will need the ZB32 GS piston. If you use the late DB/DBD piston and cannot shorten the barrel then you still have the custom rod as an option. Do you have either the piston or rod already bought?
My advice would be to first get the piston you want to use then calculate the rod you need to get made up or how much the barrel needs to be shortened. That is a straight forward calculation. You might find that you can shorten the barrel a little and still have metal to play with and make it work with a custom rod. You will end up with a compromise engine, somewhere between the long rod engine and the later short rod engines.
Maybe you could find out the pin height/deck of the various GS pistons as a starting point. I appreciate that the rod length can change the nature of the engine but the early long rod engines were winning races.