Thanks for the help, should have thought to do this myself, so now I feel a bit stupid
Booted straight away with a fresh install on another pen drive. I copied everything off my old one onto my PC, wiped the drive, then reinstalled the OS fresh using the install tool.
It still booted after this so then copied over my licence key file, and the various settings folders, and it still booted perfectly, including my array, dockers and other settings.
So pretty simple fix in the end thankfully, I was worried I was going to have set all the drives, settings, etc manually.