I don't understand why you used the loose fit bearings instead of putting the new bearings on to start with. There is no need to install and remove the bearings other than shimming the spacer, and you should be using your press to remove and install the pinion for that job, including removing the yoke. Yes, the preload will change when you change the bearings.
The marked pinion depth is almost always just a good place to start. It's always been off by around .003 when I tried to use it.