As I said before a SafeDisc protected game brings up read errors when reading. Just sit back, watch them accumulate, and around about sector 10,000~10,500 they should stop, and the reading should speed up and by the end you will get a good image. BTW do NOT use nero. Stick with just Alcohol.
The .mdf and the .mds files come together, and as long as they are in the same folder when it comes time to burn, you shouldn't have any problem.