I feel for you mate but you have to just try a process of elimination with any problem.
I will admit when i first went out on my 998R it was not setup for the roads around me but have now got it setup brilliantly.
The thing was solid from new,almost lost it the first time i took it out,the back end was bouncing about all over the place and stepped out on more than one occasion.I find setting the bike up is one of the best parts of owning a new bike.
I will agree with Jon about John Hackett,still reckon he is the man to take the bike too.
Good luck with curing the misfire.
Contact Ducati uk and see if they have heard of anyone else having the same problem.Also tell them what you have already done to try and cure it.The guy to talk to now is Tony Crawley.
I know that Hackett has four 998R's he services on a regular basis.
He has maybe got an idea of what to look for.