I can't answer your question directly, but I do have a couple of obscure thoughts for you to consider.
1. On a recent TV episode on Velocity, the crew created a shortbed out of a longbed. It happened to be a 73-87 truck...I know-not particularly relevant here, right? But, they proceeded along with the assumption of fender location as you have postured here, and all was just hunky-dory. No problem. Uh-oh, when they came back from break, they said that what they thought was true, was in fact not true. That all of the difference was ahead of the wheels. In fact, there was also a difference behind the wheels. This COULD be the case with your truck.
2. The rear axle on both the 41-46 trucks and the AD trucks have the appearance of being too far forward in the wheelwell.
So why the long-winded diatribe you ask? My conclusion would be to set the bed on the chassis and locate the fenders by eye and correct the "error" of the factory and have the wheels more centered in the opening. I would not completely center the wheels, I'd just make it better. So while the simple answer may be to just do it as you propose, I think the better answer is to measure from the actual truck, and have a result that will satisfy you.
I take it that this will be more work than you wanted to do, or you would have done it already.
