What are the steps to calibrating a machine once it is finished?

1. Square up the X and Y to each other -- no problems
2. Square the Z up to the plane of X and Y -- no problems
3 Perform velocity tests to find max velocity -- Not bad at 5inches/sec
4. perform acceleration tests to find max acceleration -- again not bad 30inch/s^2
5. Calibrate the reduction to get highest accuracy?

This is where I am stuck in a loop. The timing belts are a given pitch. I have a set gear reduction. When I enter these numbers into my machine and let it move back and forth my dial indicator is showing that the machine is out 0.001 over a half inch and 0.003 over 3/4 of an inch. This is completely repeatable and if I move it back and forth over and over and at different locations of the machine I get the same results. What do you do to dial this in? In most of my parts this won't matter, but over the length of the table I could be out over an 1/8th of an inch. Of course I don't have a dial indicator that has a 48 inch swing in travel so I can only measure over an inch. I can send the table all the way down and back and measure, but how do you know it went where you told it to?