Peace at last! Ready for War!
Great you got it sorted! I'm sure it was your data-folder, that caused the trouble.
A tiny tip: don't touch that working install anymore. And first thing: burn it onto a DVD. Just in case...
Now for every major mod you want to use, copy your entire install folder to a new location and name the folder as you like. "SH4 - TMO", "SH4 - OM", etc.
Now copy the little utility Multi-Sh4 into each SH4.exe folder and run it once for making the install use it's own data-folder.
Default folder for standard SH4 is
documents\SH4, so you may want your OM install to use
documents\SHO, TMO to use
documents\SHT and so on.
That way you can run as many SHIV installs as you like and they will never "collide" with each other.
Hope that made sense?