I’m not familiar with your journey with the Maslow, so apologies for any of this that’s going over stuff you are aware of!
My take looking at the log and what you’ve posted - your frame is too long and thin, and that combined with very high forces when calibrating is messing things up.
This would work fine if the frame, belts, and unit were perfectly stiff, but they’re not. I wonder if coming from gantry CNCs/3D printers, you’re carrying forward the expectation that as long as you can move the unit to a position on your frame, it’ll work to use that for cutting?
For me, what really helped was the realisation that the closer to a square the frame is, the more accurate it’s going to be - but with rectangular material we compromise that with rectangular frames and keep an eye that we’re not having belt angles that mess things up. And it needs the frame to be significantly bigger than the workpiece to give good cuts.
I found @dlang 's frame calculator a great resource when working out what frame size compromise to make for my work area that has some constraints:
http://lang.hm/maslow/maslow4_frame.html
If I stick in 2500*1000 as rough measurements, you can see that the areas you’re running calibration over are likely to be less than ideal for accuracy.
A quick play makes me think you could either drop the frame to ~15001000 to give you a smaller area but more accuracy in that smaller area, or widen the attachment points to give ~25001500 (or even more) and keep your calibration to a green area.
I think the calibration does a good job of calculating / offsetting skew and the stretch in the system. It does largely come down to being what you might measure but scaled down a little, but you can try approximating that yourself.
And I’ve sanded my spools down a little (What a difference 1/10th of a millimetre makes (how I got retraction to work at force 3/4/500), and I know others have - it may or may not be something that you choose to look into.