Are you sure the minor axis always aligns with the cylinder axle and goes through the 3D center? I've heard that before and thought it was weird, but when I looked it up, it sounded like it was an approximation that's only completely true when the axis/axle intersects the "center of vision". Since people generally put their focal point/center of vision directly on what they're looking at, in real life it will probably always seem true. Same for if you're specifically calling this out in a demonstration, you'll probably put the circle/ellipse near the center of the camera's view. But if you have a cylinder closer to the edge and tilted, I believe they can get misaligned, even without lensing effects. I originally learned some of this from Marshall's 1994 perspective series. Near the end of one part, in what I think was a Q&A, he mentions the minor axis doesn't always go through the center either, but it's "so close". Another source was the "Vanishing Point: Perspective for Comics" book, which says making the minor axis parallel to the axle is usually a good enough approximation, and much easier. So it's not usually important, but maybe it is if you're practicing drawing a bunch of arbitrary cylinders at various angles. It confused me for a while.

Look for curves that connect parts, Proko's demos on gesture are a good example.

It helps to construct the eyes as balls, mounted into the head. This helps you to get her left eye right...

Could you please identify the six vanishing points? I can find only five...

I like Peck's Atlas of Human Anatomy, Goldfinger's Human Anatomy for Artists, and Richer's Artistic Anatomy. There is a difference between anatomical reference, like the above, and books about drawing the human figure, like Bridgman and Vanderpoel. The former are what you need, while the latter may be useful.

You could take a look at the models by Andrew Cawrse, good but expensive.

There is nothing wrong about using whatever tool to enhance art. Just be honest about it.

Perspective looks wonky, how about leaving your construction lines for all of us to check?

In my opinion, drawabox is great for developing eye-hand coordination: I really wish I had known about this in animation school, where I realised my motor skills sucked big time, while my teachers kept repeating that I should draw more. However, after the first fistful of exercises, drawabox is less useful. The value of Drawabox is not in drawing boxes.

As a beginner, use any medium you're comfortable with. So, if you feel Krita gets in the way, leave it for now. In general, there is nothing fundamentally wrong with digital, just don't overly rely on undo. Try to get it right first time.