I don't think that there will be many parts available directly from Ducati these days that are not either NOS or leftovers, and they will probably be eye-wateringly expensive!
For end cans you should be quite lucky as most of the range (748/916/996/998) will fit with a little tweaking. You can go for either end-cans alone (which may require a different mid-pipe behind the right foot depending on size) or go for the whole system. Spec wise you will want to traditionally go with Termignoni but they have been raced with lots of other systems (like Arrows), and some with different badges on for sponsorship reasons!
For parts diagrams, Ducati normally provided these on their website: http://www.ducati.com/ducati_genuine_parts.do
However, it only started from the 996 rather than the 916. I know that there are workshop manuals available for the 916 (as I have one on CD) but these are more maintenance steps rather than parts breakdowns. Most dealers should have access to the parts system though that will give you part numbers, and a lot is also available if you search online. Some stuff will have been superseded by improved versions - which is where asking a dealer is better - or will be the same on 996,998 and 748.
If in doubt just post up here as I'm sure someone will know!