If that operation was accomplished by placing an indicator point on the table, then traversing the table, the only thing you determined is how closely the table surface tracks with the ways. If that's the test you performed, it was a waste of time.
Why do I get a queasy feeling that you may have located the holes by moving the saddle instead of the table, with the vise jaws parallel to the table front and back, but the part mounted in the vise such that it was at a right angle? If you held your part by the ends instead of by the sides, that's your problem. If you did not, ignore this comment. Do not ignore the one about the indicator and the table surface, however.
In order to determine if the spindle is at a right angle, you must spin an indicator from the spindle (slowly, by hand), sweeping the table surface. Does that make sense to you?
Unless you have need for a rotating vise, you'll find you will achieve far better success mounting your vise directly on the table. You gain head room, and often a greater degree of precision. I've seen far more vise bases gathering dust than I've seen in use on machines. They are generally avoided by those of us in the trade.
It's not necessary to do so. If your spindle that is left free isn't steady enough to use for an indicator, your setup is suspect. In all my more than 50 years on the machines, I've never had need to lock the spindle. I do advise a decent DTI for this application, however. A Starrett last word is not amongst my recommendations. I own one, along with several B&S BesTest indicators. The Starrett never gets used because it lacks the necessary precision. So you'll understand that I'm not bashing Starrett, my toolbox is almost entirely Starrett-----my only complaint is the Last Word, which is a disgrace.
Harold