I keep getting this message when I run the INSTALL: "Volume Workbench 3.1 Full?"
Never never never never select "Novice" mode when installing something with the Amiga installer. Always use "Advanced" or "Expert" mode. In this case for example it would ask you where to install to and not silently try to install to the floppy disk.
And always keep your original floppy disks write protected. I don't know if the Gotek supports this, but you should try at least.