The longer the distance you can measure from, the more accurate of an idea you're going to have of how far off you are. Can you put a sheet of material on the table (preferrably something heavier so it can't shift around) and position the head at 0,0, use a framing square against the sheet and head and mark the position.......then command it to move...say 40 inches or so in the X direction and mark that position with the framing square and use a tape measure over that 40 inches to see where you're at? If you have someone who can hold the dumb end of the tape measure exactly at the 1" mark (instead of trying to use the hook) you should be able to get a pretty darn accurate measurement. NO, you won't be able to see thousanths, but over the length of 40", if one end of the tape is dead-nuts on 1" and the other is not dead on 41", at least you'll know which way you need to go and approx how far. Once you get both marks to be dead on with the tape measure, you'll most likely be accurate enough that....well, it just won't matter.
You're going to be able to measure the accuracy of the machine a lot more accurately over a 40" span with a tape measure than you can over a 1" span with a dial caliper. Using your example, if you're off by .004" for every inch, in 40 inches you're going to be off .160"......you'll definitely see that on the tape measure with no problem!