I know its not for the 998s but I found this the other day and found it quite usefull. Its for the 748 and only gives part no's but it shows how most of the bike goes together. For the non mechanic types (Like me) it was a good find.
I got a factory manual from my Ducati dealer it covers the Testastretta engines ! Wil post the part No if you want I think it was about £25 I have the Haynes manual for any other info !
Still looking for the part No , had it written down some place ! If you need anything scanned ,or if you really want i could mail you the manual then you could photcopy it , although its a good few pages On the front is says Testastretta per 996R/998 engine