I also turn the chuck by hand when I'm chasing threads on Mausers. Just chicken I guess.
It is SOP to drill the rear hole for the front scope base, ahead of the locking lug abutment. Given the location of the slots on your bases though, you can be forgiven for locating it where you did. It looks good. At the rear, it is normal to locate the rear base so it is even with the front of the bridge, but this can only be done if you slot the clip charger hump and inlet the base into it, or remove the hump altogether. Again, your install looks pretty good though, so it's hard to criticize!
Using soft jaws and tapping a piece into alignment is truly advanced machine shop practice. I have also used shims to achieve alignment in some cases. Of course, you could spend a few hours making a jig to do the same thing! WH