The '03 749 and 749S have the same engine as each other. The S has full Showa suspension and titanium nitride forks, plus a Showa steering damper. The 749 has a Boge rear shock and damper, plus lower spec Showa forks.
The '04 749 and 749 Dark have the same engine as each other, which is the same spec as the '03 749. Chassis spec is the same as each other, but the Dark doesn't have a steering damper. The '04 749S has an upgraded engine with a touch more power. It has different cams and a higher compression ratio.
There are no major problems except for the usual used bike things. The only extra problem I would watch out for is stalling on idle on an '04 749S. They seem quite prone to it happening, but usually early in their life (under 1000m). My 749S started doing it at about 1200. It's fixed by getting a dealer to set up the cam timing correctly - they need a very accurate 'tool' of some description that was issued by Ducati after the first cases were reported.
Depending on the model of Termi fitted, they can add a few quid to the bike. I think the most popular is the asymmetric system (basically a slip on) and this would probably add about £500 to the price of the bike.
Hope that helps! A test ride on a 749 will probably sell you