As I finished typing this I thought that instead of indexing only on the previous holes perhaps we could index on the center of the disk (even if the center hole can not be done in the mill). That way the radial distances would be safe from drift and the errors would only accumulate "in the angles" as we "release", "rotate 360/16" and "clamp".
Hmmm...
Does not fit in the planned enclosure I guess I'll need to take the front of it off or something.