B. It's a server that I built using standard pc components but enough to cope with the needs of freenas
That doesn't answer the question. What "standard pc components"? What motherboard, CPU, drive interface (if any), RAM, etc.?
C. I am unable to ssh into the server as it won't allow me but if I go to the shell cmd prompt and input zpool list it comes up with only the working drive
What do you mean "it won't allow me"? Is SSH turned off? Then turn it on. Does it give you an error? Post the error. In any event, even if the web GUI's shell is the only CLI access you have, you can still copy from that and paste it here. To repeat
@pirateghost's question, what is the output of 'zpool list' and 'zpool status'? And I'd add to that, the output of 'zpool import', 'camcontrol devlist', and 'gpart list'.