YSmenu is an alternate interface for the DSTT. You build it using the regular firmware so it really shouldn't make a difference in compatibility, but you never know.
As for getting CT to run, instead of patching the rom, try using AR codes. Make sure you have the original unpatched rom. Then go to cheats.gbatemp.net and download the latest USRCHEAT.DAT file and copy it into the TTMenu directory on your sd card, overwriting any older version. Then before starting CT, turn on cheats and go in and select the cheat that fixes the problem.