When bareshaft tuning a new shaft, how does one know the difference between the nocking point either high/low or if the shaft is over or under spined.  It seems to me that one could give a false reading for the other.

Start with your nock point high....3/4" or so. That way you don't get a false reading. Work on getting the spine close, then work on the nock point.

Most of us traditionalists shoot our bows with some degree of cant, however when bareshafting it's best to shoot your bow held vertical (no cant). That way you won't confuse spine readings (which will be horizontal deflection) from nocking point readings (which will be vertical fishtailing). I agree with A. S. in that you atart with a high nock point, so your arrow will fly nock high. Ignore that initially and first concentrate on getting the spine deflection perfect. When you have the correct spine (obtained by altering point weight or shortening your arrow shaft)then start lowering your nocking  point until you remove the fishtailing from the bareshaft flight. Bingo you're done!