When you've booted from an external. Try these instructions to split the fusion drive, then clone your OS back to just the SSD from your external disk.
http://www.macworld.com/article/2015664/how-to-split-up-a-fusion-drive.html
Might help, might not but it's worth a try to have a working system. If you're using for audio, assuming Apple don't absolutely screw their customers by marrying up a fast SSD with a bargain bucket 5400rpm HDD, you could actually partition the HDD as a recording drive once you're booting off the SSD.
Something like this:
Macintosh HD: 128Gb SSD.
Audio: 100GB (or whatever size you choose).
Storage: Remaining HDD space.
http://www.macworld.com/article/2015664/how-to-split-up-a-fusion-drive.html
Might help, might not but it's worth a try to have a working system. If you're using for audio, assuming Apple don't absolutely screw their customers by marrying up a fast SSD with a bargain bucket 5400rpm HDD, you could actually partition the HDD as a recording drive once you're booting off the SSD.
Something like this:
Macintosh HD: 128Gb SSD.
Audio: 100GB (or whatever size you choose).
Storage: Remaining HDD space.