ok first Mpeg3s, for your games that arent selfbooting properly, this method probably wont affect your efforts that much.
As far as i know this method simply uses a sort text file to organise the cd layout exactly like the GD rom. This is usually just done to ease loading times and reading problems for the GD Rom drive like for KOF. Your best bet is to post which games your having problems with. (some games require extra modifications to the .bin files, like F355 (thanks megalexxx again for that
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Silmariis, If you use the CDRWIN method then your msinfo number will be 11700, or something else if something goes wrong, which is unlikely so use 11700. The 11702 number is if you use cdrecord.