Well the jaws are case hardened to 60 Rockwell as far as I know, so I'd give up on the idea of a tapped hole unless you care to thread mill after drilling. I guess if you wanted to mill .125" off with a coated carbide endmill where you wanted the hole, then you could drill and tap it. The keyed block the back jaw bolts to is soft, so you can machine that and make a stop from there. I have also made a bunch of M6 holes in the side casting to mount a universal stop I bought from US Shop Tools. (I gave up being worried about the vise's resale value).
Sweeping the indicator over the 6" long jaw will tell the tale. If the jaw is damaged and is no longer flat (unlikely), the indicator will show it. If the vise just isn't square, the indicator will trend consistently in one direction in a very linear fashion. This method takes out sources of error like the indicator holder moving slightly this way or that. You would see that on a reversal of travel, but not in the middle of a sweep. Also, putting the Bridgeport in low gear takes care of most spindle movement. A magnetic base on the quill would take the spindle out of it altogether.