If you use the method I showed you it doesnt matter what your mic says as you are eliminating it from the equation. Only tooling error you will have is from the actual bore gauge itself. Now this way will take more time as you recalibrate your bore gauge for ever single journal.
Bascially
Measure journal, place outside mic in vice, calibrate bore gauge to micrometer and then measure bearings in block to get bearing clearance.
then move on to journal #2, measure the journal, place in vice and calibrate bore gauge and measure bearings in block to get bearing clearance.
repeat for the remainder of the journal, do same for mains and rods.. takes a bit of time, but the error in the outside mic is eliminated this way.
hopefully that makes sense to you