I have a da vinci duo, and learned the hard way how to calibrate. I had the same issues - the literature that came with the machine warned me not to calibrate (since it was calibrated at the factory). Very soon, the extruder(s) were hitting the model and the the nuts started falling off, so I had to learn how to calibrate.
This is a very long post, but I wrote it to help others understand that if you create a repeatable process for yourself, calibration is a lot less of a hassle, even if what you are doing seems random and or backwards at first.
I created an excel file to remind myself that the three numbers displayed are in order:
Back (right), Right (front) Left (front)
and refer to the corners that the autocal measures in this weird Back, Right, Left sequence.
There are three support nuts - NOT where the corners are, but in a triangle. The 'back' nut is really in the middle of the plate! I taught myself to think about the three nuts as:
Back, Right, Left
And associated them in my mind with the three values.
The Back nut is kind of on the diagonal between the left front corner and the back right corner. So . . . I'll return to that in a moment . . .
I realized the easiest way to think about turning the nuts was that if you put your thumb to the left of a front nut and rotate it to the right until your thumb hits the edge of the plastic surrounding the nut . . . that's about a 1/4 turn. I think of it as rolling to the right. I have to 'roll' the left and right nuts, but I can grab and turn the middle nut 'the back nut'...
When I turn the 'back' nut, I position my thumb and forefinger at 45 degrees on the nut (they are now on a line from left to right), and twist it through a 'roll' that puts my fingers on a new line, 90 degrees from the first (they are now on a 'front back line'). This means that I can roll the back nut through a quarter turn, just like the front left and right nut. It really helped me to turn (roll) all three nuts the same amount.
ROLLING TO THE RIGHT RAISES
I then, through a lot of repeated effort, understood that everything is backwards.
If a number is higher than the target (for the duo the target is 100), then you have to raise the nut associated with that number to lower the number.
To raise the nut, and lower the number you roll the nut to the right.
To lower the nut and raise the number, you roll the nut to the left.
I visualize the plate. If the number is 90, 100, 90, then the left corner and back corner are at the same height, and are low, meaning that those two corners are closer to the extruder - they are high. If you can get two numbers close to the same value, you can then concentrate on the other number.
Having a good imagination is crucial to not going crazy over the headache of calibration.
so . . . back to the fact that the 'back nut' is not on the back of the plate. It's really in the middle of the plate. It's only 'back' in the sense that it's away from the 'front' of the plate. - this is where some imagination helps - Picture the plate as having a hinge when you calibrate. That hinge can be along the front of the plate, or it can be along the diagonal between the left (front) and right (rear) corners.
It can also be along the diagonal between the right (front) and the left (rear). but most of the time we can ignore that. All we really need to do is to pair two of the numbers and adjust to bring those two numbers closer together.
Often I'll get a result of 139, 90, 80, meaning the back is low and the front is leaning to the left. Since 90 and 80 are close, I'll ignore them and work on getting the '139' closer to the other two. If the right and left numbers are close, then the hinge is along the front edge. Raising or lowering the back nut will open or close the 'hinge' and affect the third number, while having a minor effect on the other two. Remembering that a larger number means that part of the plate is lower than it should be, I roll the back nut to the right, which will raise the back towards the extruder and decrease the number. It would have been so much more intuitive for me (on the West Coast of the US) if the numbers followed the direction of the nuts. The engineers in Taiwan probably find it intuitive just the way it is . . . but whatever. Culture is different depending on where you are in the world - you just have to live with it.
I used the spreadsheet to keep track of my moves and keep track of the result of the move.
Eventually I put a label on the front of the printer to remind me.
Actually I put two labels on the front with arrows, but I think I'll replace them with the simple statement:
ROLL TO THE RIGHT RAISES
That phrase helps me visualize the bed of the printer. If I need to raise the back, or a corner, I roll the nut to the right. If I need to go the other way . . .
There is probably a Chinese phrase that makes perfect sense and associates the movement of a nut to the change in the number. If I understood Chinese it wouldn't seem backwards to me
So instead of getting hung up with the numbers being backwards to the direction of movement of the nuts, I concentrate on translating what they mean.
Back, Right, Left
156 35 90
means the right corner is too high (relative to the left), and the back of the plate is too low. The left is sort of close to the target, and I can ignore it for now. So I'll roll the back nut to the right to raise the back and roll the right nut to the left to lower it.
I found it really helps to have something else to do while calibrating. I'll start an autocal, go in another room and focus on some small task, then return to the machine when it gets quiet. Do another round and do some other small task.
This means I get about 15 minutes of work done on something during the 30 minutes I'm calibrating the printer. Watching TV helps, or watching YouTube. I can go back to the printer during the commercials, or between videos.
But wait! Why does the rolling the nut in one direction sometimes appear to have a random result?
There is a spring between the bed and the nuts. Sometimes when you turn the nut, you turn the spring too. This creates a movement of the spring end on the surface of the nut or the underside of the bed. When this happens, you get a result that is totally unexpected. 1 quarter turn typically changes the number by X . . . except when something moves that you didn't want to move (like the spring). Instead of just compressing it, you turned it and it resulted in an unexpected change in the numbers. I may introduce a couple of smooth washers into the stack between the nut and spring and the spring and the bed and see if that helps make the movement of the nut more regular.
If it works, I'll post it.
Engineer in the Medical Device Industry, used high end 3D printers, but exploring what can be done with inexpensive printers. Own a Da Vinci 2.0 Duo