Thank you for posting the images.
First, let me annotate them:
Note that the slide contents and the hard vignette due to the field stop stay in a nearly fixed position in all three frames. That tells me that you did not change what I'm calling "tilt".
Attempting to illustrate more clearly what I'm talking about, I have shot some images and prepared what I hope is an understandable explanation.
First, here is the setup -- simply a cell phone held carefully over the eyepiece of a binocular microscope:
Then I misaligned the camera in various ways, shot the images that resulted from those misalignments, and put them together into this explanation:
The light coming from the eyepiece forms a sort of hourglass shape. It is important that the camera is positioned so that the narrow part of that hourglass lines up with the aperture of the lens, so that all the light from the eyepiece can get through the lens.
The camera also needs to be pointed straight into the eyepiece, so that the center of the field goes to the center of the camera sensor.
If the camera is perfectly aligned but zoomed too wide, it will see part or all of the field stop that is built into the eyepiece (top left image).
Holding the camera still perfectly aligned, and zooming it narrower, the image expands so that the entire field stop lies outside the captured frame. This is the ideal situation (bottom left image).
On the other hand, if the alignment is not correct, then I get various forms of vignetting. Hold the camera too close, and I get a big fuzzy vignette. Hold it too far, and again I get a fuzzy vignette, though maybe smaller and sharper. Tilt the camera to the left (or up, down, or right), and the camera sees the field stop in the eyepiece, at the same time that the image shifts within the frame. Shift the camera sideways, but keep it pointed straight down the eyepiece, and again I get a big fuzzy vignette but this time it's not centered. Of course I can commit multiple sins at the same time, such as simultaneously tilting and shifting the camera to both see the field stop (sharp vignette) and block part of the light cone (big fuzzy vignette), as shown in the lower right.
So now, analyzing your images, it looks to me like they show just a slight tilt that is almost constant, with varying amounts of mostly shift that causes a fuzzy vignette to march across the frame.
All in all, there's a lot that can go wrong. You need to have the camera located at the correct place (X,Y,Z), pointed straight down the eyepiece (pitch, yaw), and zoomed enough to miss the field stop. That is six things to get right, all at the same time, and errors of even 1 millimeter can produce nasty effects. If somebody doesn't understand what's going on, this can all look completely random and incomprehensible.
So, I'm highly sympathetic to your confusion!
That said, all this is neither black magic nor rocket science. What you really need to do is to calm your frustration, stop thrashing around, and start paying very close attention to how the image changes as you move the camera around by small amounts.
I'm not at all surprised.I got that weird flickering again in the LCD screen where extreme vignetting occurs about every second, accompanied by a clicking sound.
I would place a heavy bet that when you get the alignment under control, the weird flickering will start to make more sense. The extreme vignetting accompanied by a clicking sound is caused by the lens iris suddenly stopping down. That's a transient effect triggered by sudden big changes in the amount of light getting through the lens, which is caused by shifts in alignment, which you don't have under control yet, so the problem seems random. It doesn't occur away from the microscope because then the camera doesn't see those sudden shifts in brightness. With my cell phone the effect manifests as overshoot and hunting in the automatic brightness control, unless the alignment is near perfect. (Yes, I understand that you have intended to set the camera on "full manual". But it seems that the camera's view of what that means is a little different from yours.)
I hope this helps.