The clone could work as your boot drive until you solve the problem with your Fusion drive.

Yes you can plug your Time Machine Drive into the back of your computer and use it as a disk drive. You could even put your User folder on it following these instructions. You cannot however use it as the HDD portion of a Fusion Drive — that is not supported by Apple for numerous reasons.

If we knew what it was we were doing, it wouldn't be called research, would it?

— Albert Einstein