OK, reread the bore gauge part... 3 clock positions, not the 3 o'clock position
I use a Standard Gauge dial bore indicator, and yes, it might leave a mark on the bearing, but it is not scratching it. Your indicator needs to read to .0001 (tenths) to measure accurately. If you are using telescoping bore gauges and trying to measure those with a mike, you might be giving up some accuracy.
Good luck with your project.