The best way to measure those holes and be truly accurate to .0001 is with bore gauges and setup masters (this is completely ignoring all environmental variables as well).
Quality gauges taht are certified this accurate will cost MANY MANY thousands of dollars.

As far are processing these to size with YOUR setup, I would bore them really close undersize (.0001 - .0005) and hone or lap them to finished size.
These holes would be easiest to size in a lathe, but setup would be a lot of work.

Otherwise - get a jig grinder.