Thank you for the images. Something is not quite right, there, especially with the first image (fully zoomed out?). Could I trouble you to repeat the experiment without the barlow lens? I like to take images of graph paper, in sharp focus at the center, as the grid also help show aberrations.
More camera friendly stereo microscopes – or their add-on photo tubes – include dual apertures that let you stop down and win more field of view. The ones I am familiar with are, I think, around f7 when wide open, and do not give much depth of field unless they are really stopped down, noticeably dimmer and starting to lose detail. I can see why stacking has become so popular.
If you think of the microscope as the lens, I tend to the notion that you want to stop down, and for that you need much more light on the sensor and a sensor that needs less light. There is a fair amount of art in getting that – which I am learning – so I am not sure what to suggest.