Glad it finally worked for you.
If your back-up copy is working fine, there's no need to retain the mdf/mds files unless you want to have the alternative of running the game from a disc image mounted on a virtual drive. Unless you want to have that option you can just delete the image files which are taking up a lot of valuable space on your hard drive.
As for whether you should shell out for one of the specialist duping proggies, well only you can know whether you want to copy enough copy protected cds to justify the cost.
There are no free alternatives that can handle the majority of currently used copy protections in conjunction with nero though there is a freeware dumping tool called discdump that can be used together with nero to copy (with suitable hardware) any safedisc 1 and all versions of safedisc up to 2.7 (significant hardware limitations for sd 2.51+ though) and which has some success with nero for sd 2.8 and 2.9 too.
The same combination can also be used to copy laserlock protected cds (do the dumping overnight though) and sometimes works for Ring Protech protected cds. Securom (all versions) is out of the question though.