I've gotten to the point where I can extract the original files with GARbro but I can't extract the patched one that HMFan made. If anyone else wants to give it a shot, here is the extracted scenario files for Yuugi.
https://files.catbox.moe/sj2gi0.zip
Did some extra digging and found that you can indeed repackage the files with arc_conv
https://github.com/morkt/GARbro/issues/417#issuecomment-1007078043
https://github.com/amayra/arc_conv