Well i've had the wire cutters and soldering iron out and have now had the engine turning over on the button, very slowly as the battery is as flat as a flat thing can be.
I also had to reconfigure the clocks wiring harness to get the neutral light to work off the later engine.
Once I'm happy that everything is wired correctly it will be time to lengthen the harness by 70mm or so required.
Kev
PS also found a wiring diagram in the 998FE owners manual in PDF on
www.ducati.com