I've got a Ducati 749S (2003) that's recently developed an intermittent misfire. Last run it went onto 1 cylinder for a couple of seconds then cleared, then the same happened again. It was then fine all the way back (40 odd miles). Started up fine this morning, after about a mile it went onto to 1 cylinder, backfiring then would chirp back onto 2 cylinders then down to 1 again. Managed to get it back virtually 1 cylinder all the way (1 mile ). Had a good look over it but nothing seems obvious.
Not had any problems myself, but, have heard many many 749 and 999 owners talk about problems with coils / spark plug caps. Seems the front one is the obvious one, gets hit by all the crud from the front tyre.
Take it off, give it a good clean, loads of WD or similar and put it back.
I'm sure someone who has first hand knowledge will be along soon.
Mood: Out with the grey....in with the satin black
As mentioned already, it does sound like a faulty coil. You can tell which cylinder isn't firing by checking which exhaust pipe isn't getting hot. Once you've identified the problem cylinder, remove coil & clean as suggested above. If cleaning doesn't work, I have a spare pair of coils (used but work perfectly) & would sell one of them. Let me know if you're interested.
Fault :- Water in the plug holes clean coil and plug tops (these may even be loose) spray with wd 40 and seal with silicon jobs a good un! do not buy new coils until you've done the above. Mines done it several times before I sealed them up.