There are many issues with building a machine that is accurate and true to the axes (Square and flat). Industrial machines are built using lasers and master squares for alignment and flatness. Even large, heavy cast iron machines exhibit twist along an axis which has to be taken out with "leveling" the machine.
For accuracy, the ball screw is what will control positioning and accuracy. The cheap ball screws we use on hobby machines are rolled threads, not ground. They are very economical for a reason, they are NOT accurate like you would find on an industrial CNC machine. I would not trust the accuracy of a rolled ball screw to anything less than .003" / foot of length.
Using an old Tool Maker rule that I believe still applies today...
If you need +- .002" you better have an accuracy in your 'tool' that is 10% of that amount or better. Tool in this case is the machine and thus, if you want to hold +-.002" you better have a positional accuracy of +-.0002".
Chris D