I wonder why people want to convert selfboot games to non boot games just to add a dummy. Sometimes, things are just too easy; people need to get them complicated.
Anyway, a bit of theory.
What makes a DC CD selfboot ?
1) 2 sessions, because DC looks at a file located in the boot sector of 2nd session (ip.bin)
2) a small value in 1st_read.bin (8 bytes before "CD001") that tells the DC where to find ip.bin (LBA value). This value can be modified with binhack.
So, if you want to convert a selfboot game to a non boot game, simply extrat all your files to a directory (using windows explorer for example), create a correct ip.bin and burn all your files just as it. I'm not even sure if you need to binhack 1st_read.bin...
BUT, if you only want to add a dummy :
1) extract all your files from your CD (windows explorer if you already burnt it, or CDMage if the image is supported, or CDIRip + ISOFix + CDMage if it isn't)
2) extract CDDA if there are some (still CDMage, or CDIRip, or my tools :
http://home.tiscali.be/nomax/PALPatcher/ if it's a CDI image)
3) create a correct ip.bin or extract it from your image (with CDRWin or my tool). You don't even need this step if you use Bin2Boot...
4) create your dummy file
5) follow Echelon's tutorial to make a selfboot game, or use Bin2Boot.