My old Zeiss GSZ stereo microscope was way out of alignment when it first arrived via courier and was unusable as a stereo microscope.
I think it must have been dropped in transit and knocked out of alignment. I ended up taking it all apart and I aligned up everything to get the stereo action as perfect as possible.
There are lots of subtle places you can adjust the optics. I had to perfectly align the zoom and there were other adjusters inside the microscope. It took a lot of work to get it right.
Once I got this all aligned I found I could just look into the microscope and get effortless stereo alignment. You will know if you have it wrong because your vision system will have to fight to compensate for any imperfections and your eyes will tire quickly and also your vision will be a bit wonky for a while after you look away from the microscope.
My microscope went from being completely unusable as a stereo microscope to one of the best in terms of how effortless it is to get stereo vision. I can now just look into it and see stereo perfectly without any need for my eyes to do any compensation to align the two images. So I can use it for quite a long time without fatigue