OK - I fixed it by doing the following:
I ran the set_empeg_max_fid which I hadn't previously done.
I ran the fidsift.sh program.
Still no joy.
I then deleted the contents of all the _0005 & 6 fids directories to get the contents back to about 15k tracks (120GB used).
This then let the machine boot OK and rebuild the database and then jEmplode (v69) managed to re-sync OK.

I'm now going back and putting in what I think is missing and we'll see if it craps out again.