If all of the machinists just had the shaft & its parts, I guess I can't blame them. I wouldn't & couldn't do that either. It would be a crap shoot with nothing to measure from.
But, with the crank & half of the case you can measure from the parting lines of the case & get them exactly where they need to be. The weights need to go 180 degrees to the piston stroke, it's not that much of a science & easy to figure out with the right tools. If you take a look at the weights you will see that they are just cast, its not balanced as an assembly.
Seeing your being thorough, drop your crank into the case. Make sure the bearings are fully seated & index the crank to bring the rod pins perfectly centered on the parting line. Then with a straight edge, check where that edge meets the gear.
Does it land on the tip of the tooth, in the root, or somewhere in-between?