I use CloneCD for backups, and I know for a fact version 4 gets past SafeDisc 2, and I think it will get past 2.5
However the key is setting the right options. For making an image file, you need to check/enable "Read SubChannel Data" You'll also need to turn Fast Error Skipping on, and disable Intelligent Bad Sector Scanner.
When it comes time to write the image, you'll need to enable Amplify Weak Sectors. You'll also need to check the box that says Don't Repair SubChannel Data.
Also, it is adviseable that you don't read or burn at maximum speeds (so if you have a 32x12x48, you may want to write at 24x, instead of 32x), and always use high quality CD-Rs (iMation makes good discs)
There are some newer protection systems like FADE and TAGES, which are becoming a bitch in the gaming community.
What would really help people out is a proggie that would allow people to create, edit, and access the lead in and lead out areas of CDs.
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Benchmarks don't lie 🙂