The old timers were pretty good. Also, there is a big difference between making something new and trying to save as much old stuff as possible. I sort of doubt that any of this stuff would be saved in a proper, well funded railroad rebuild. If the RGS did it in their usual financial situation, they would have probably just taken out some of their paper shims and adjusted it as close as they could. Probably would not have replaced the cracked link since it might have given a few more years before breaking. Compensation in timing would have been made if needed to make the engine as square as possible.
New link halves would not have been that difficult to make with the tools of the time. Probably the reason they went with built up links. They would be easier to make albeit not as rigid in service.
We will still have discrepancies in dimensions insofar as pin placement. They are small enough not to worry about and not worth trying to make perfect. The new link will be a compromise between where it is supposed to be and where its mate is.