Thank you for your perseverance!
I shall deal with the simple part first: Your stainless steel nuts are made to the DIN934 standard pattern, the brass nuts are not. To fit in the body you will need brass nuts to the DIN metric full nut standard, 5.5mm across flats and 2.5mm thick.
Your other problems are slightly intermittent, which makes them very hard to diagnose - a lot of your scan looks fine. The essence of what you have shown is that the stage clearly does move in x and y, and is able to focus, so it is moving in z as well. However you are seeing motion that is not quite as expected.
Wear from the steel nuts and steel screws in the actuators could give these symptoms, but you would expect that to have got worse over time, and you saw problems early. The wear can be very quick if you are scanning and have not got lubrication. You need very little quantity of oil, but it does need to be in the thread where the screw goes into the nut.
When you say that you swapped motors and it did not solve the problem, did you swap for three new motors, or did you keep the same three motors and swap which axis each motor was on?
When you have disassembled bodies, have you noticed any issues at the base of the actuator columns? One of your earlier posts has the columns detached where you took it apart. The base of the column has quite a lot of force on it and relies on good layer adhesion to remain in contact. Others have seen breakages in that area, for example the first image linked in the first post on the thread Does this mean I have to reprint?, and the solution in Microscope v7 stage is jumping / skipping / rewinding was that the hex bolts were too long and had pushed the bottom off the actuators. These symptoms are similar to yours. If you have a body that has had problems could you look at the area at the bottom of the actuator? or remove a foot on your problem microscope and post a photograph? You say that you are new to 3D printing and that there were problems with your tool print etc. Layer adhesion depends on printer setup and tuning. It is not something that I have needed to attend to so I do not have advice on what parameters to change, the printers that I have bought were all well tuned already.
The other question is how much you see this problem when moving the stage with keyboard commands. Is there always a problem, or only sometimes? Does it happen more when the stage is far from centre? Is it a jumping/skipping (like Microscope v7 stage is jumping / skipping / rewinding) or sometimes just not moving? This will give more detail of the issues than the scan failures where there are many things going on at once.