Hi @dougf I had a bit of a break, I’ll try to go through all of your questions. I hope I have not missed any.
Arduino Nano/Uno: Both boards are based on the ATmega328P so as you have found there should be no problem with installing the Sangaboard firmware on a Uno instead of a Nano. The Nano is just smaller which can be more convenient. Re the comment from @mzedp on the pin direction, the Nano pins should be in the usual direction for a Nano, as for the soldered header versions that are available. The Nano then goes upside down with the pins in the air.
Video display: There are two ways of putting the video feed to the display on a Raspberry Pi. The fastest is to directly feed the video from the camera to a region of the screen. This is GPU preview in the Openflexure interface, under settings > display. As you have found, it places the video over anything else, which can be annoying if you are using the Raspberry Pi desktop, and particularly when you are doing the initial setup. The other way to display the video is to send it to a web stream which can then be viewed on another device over the local network (or on the Pi itself as the Openflexure interface is actually a web app running with a virtual network connection). The web stream goes through processing and sending over the network (or virtual network) so is slow to update, but it is under the control of the interface so is kept in the window nicely.
That is all a long explanation, what you need to do is uncheck Enable GPU preview and uncheck Disable web stream in settings > display
All being well this will help with the other issues as you will be able to see what you are doing better. the other errors might all be related, but it is a little hard to tell. As you say it can be hard to tell exactly where the issue is, the log file might help which you can get from the Openflexure interface under logging. However, in practice these types of issue usually stem from a corrupted installation somewhere in the Raspberry Pi operating system or the Openflexure Server. This is a weak link in the Raspberry Pi, partly because SD flash cards are actually not very reliable. My first thing to try is always a fresh installation of the SD card, or even a fresh SD card. Then ofm update and ofm upgrade to make sure that you are on version 2.11.0 or higher (I think that is the latest version). See whether that solves the problems.
Note: ofm serve should not be required, it is for development only. I am not exactly sure what it does, but you may have ended up with more than one instance of the microscope trying to run at the same time.
Camera stage mapping: The camera stage mapping is actually not really needed for operation of the microscope. It just lets the software find out the relationship between the size of a motor step and the movement across the screen image. This is used for ‘click to move’, where you can click on a part of the image and the microscope will move that to the centre of the image.
Pi version: Is it a Pi 2B that you are using? This should work, but I have not recently tried a Pi 2 on the microscope software. A Pi 3B is significantly more capable.