If it's this close why not spend a bit of time to get it spot on? I'm retired so time spent isn't a problem. I'm just not certain what adjustments to work with for this minute fitment issue.
Joe
when you level your build plate, you use a piece of paper and are adjusting manual dials and using the friction amount from pulling the paper (at least that is how I zero my bed). your tools for calibrating are at best a paper thickness worth of accuracy...
Not only that, your printer is probably using a mechanical switch for the z-zero switch. I again doubt that switch is going to give you repeatability better then a thickness of paper.
This is why I said to print a larger calibration cube, which will help ID if this is a scale issue - something you can adjust for, or an equipment precision issue - something that you likely can't adjust for.
Another thing you could do, would be to print 5 calibration cubes and see if they are all the same size. I would absolutely expect a small amount of variation between them.
Honestly, right now it sounds like your expecting more out of a home 3D printer then is reasonable to expect. if your that close in tolerance already, your talking about very fine levels of adjustments needs to get it just right. Not only that, your stepper motors have a limited number of steps that they can make, so there is a minimum resolution to the printer no matter how well you tune everything (assuming there is anything that can still be tuned out).
So your asking "what can I adjust to get more accuracy then seems reasonable for the equipment?" and we are answering "it looks like it is probably as accurate as it gets"
If you really think it can get better, print a 40x40x40 cube and see what it measures, this will help us ID if you might have a scale issue or precision issue. then 2 more 20x20x20 cubes and see what the variation between them is. if your variation is close to the amount of error, you have hit the max accuracy of the equipment.