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Taking a look at the PC-98 version of CTR... Holey moley. There looks to be nothing shared between the windows and PC-98 versions. Even the DAT file format isn't the same, though it looks deceptively similar. And when I looked through the disassembled SGS.COM, nothing really stood out as familiar. Not promising.
You mentioned minor glitches... Did you see anything other than the fades glitching?
The fading problems you mentioned, and inconsistencies when rapidly changing the background (might be a framerate slowdown of some kind.) Saw it happen in V12's Magical Gambler stroy when Sai holds up the wand and the background alternates rapidly.
Think you could make a version that doesn't use the SGS.DAT file? and looks directly for the START.WINThat's how I'm used to working with Viper games. I modified RSR's SGS.EXE to work with uncompressed files.
Yeah, it does more than that: it activates internationalization, that is, loading strings from text.jp/us/it/dh/sp and using different fonts. It was failing on your script because text.jp (the default) was not present. I've updated it to be more forgiving. You can get it from http://www.sendspace.com/file/6rfxpk