Start with something like the thin walled 20mm cube. Print that until you're confident you've determined the extruded width for a height, and really dialed in the extrusion temperature, and some of the backlash.
Now move on to my calibration block. Print with your starting settings.
Once it's done, now is the time to really bust out the calipers and calibrated eye.
The thing that was most obvious to me after my initial print, was the deformation in the column coming out of one of the blocks. If this appears squished, bulgy and deformed, turn on the cool plugin, but set the time limit low, on the order of around 10s(PLA). This one is key, because if your column is deformed or squished, the outer diameter on the stretch will be inaccurate.
Now, examine the bridge, if it is slower, then go to speed, and configure feed and flow rate ratios for briges to be something lower, for instance my setting turned out to be around .75.
Now, look at the top surface of the blocks. Are they particularly ridged, like they're overflowing? If so, you have not calibrated your width properly, so your w/t is too low. Are the ends of the infill strings not touching the perimeter loops, then it's the opposite. Careful here though, as infill w/t is judged much more by the springiness of your material, so you may just want to change your infill w/t.
Now, get to the holes, if they are too small; small holes should be 3mm, big hole is 10.2, column is 10 hex is for m3 nut; then you need to raise the stretch factor. Too big, go the other way.
Last thing you want to look at is backlash. As a mechanical guy, I tend to say if you have backlash, it's your belts adjust them, but the software side of me says you can fix it with the lash setting too, just use calipers to measure the difference in the column diameter to get the backlash, though this does assume one is correct.
This has been the best calibration piece I've used so far, but please I welcome feedback. Also, I wrote up these instructions probably a bit too fast....