Good morning Ian,
Welcome to the
the world of pain (and cost) that awaits me.
As a Ducati twin owner you are already familiar with some of the foibles of the beast and the folly of keeping a stable of them!
Your assumption is correct!
What am I going to have to re-shim (I'm assuming everything)
As for the order of this time consuming, theraputic art of shimming; check that the cases are square and the holes are true (Nigel Lacey has found many aren't), con rod in the crank, crank in the crankcases, gears on the mainshaft, gears on the output/layshaft, gear shafts in the crankcases (with the shimmed crankshaft in place), selector drum in the cases (with the shimmed crankshaft and gear shafts in place), shim the gears in the timing chest, shim the oil pump drive to the timing chest outer case, shim the gears/cam in the cylinder head, shim the rockersin the cylinder head, shim the clutch outer case bearing on the end of the crank.
I suspect that others will be along to remind me of the shims that I have forgotten. Nigel Lacey or Eldert probably do the job in their sleep.
Ducati OME, Clymer or Haynes manuals, I use all three are essential and a notebook to write down all the shim values that you set your engine too. Then you will know for next time.
DO NOT REMOVE SHIMS WITHOUT REPLACING THEM ON THE SHAFT FROM WHICH THEY CAME!!!!! 
I have been asked to rebuild a stripped motor, in which all the washers and shims were in a separate tobacco tin, with the passing comment "I thought that you might need these as well!"
Finally, if you are not sure try using the "Search" window in the top right of the screen, or ask, this forum is a font of knowledge and experience.
Good health, Bill
