Did you load the MODS with JSGME. If you did use JSGME then you can unload all the MODS and do a file structure compare to the snapshot you took on the clean install of SH4 prior to adding mods. If the snapshot comes up bad then your install is hosed and you need to re-install.
Sounds to me like you need to re-install....I could be wrong. Post more details, please.
Good luck.
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