It's very strange. I like the theory of something getting screwed up when I changed to a TMO only setup, but I think I already did just what you suggested. I deleted the files from JSGME, deleted the game files in SH4 and brought in a Pristine copy that I keep in a separate folder, deleted the Rich and Save game files, moved a pre-set group of Mods for TMO only to the JSGME Mods List via the MODS folder, and then restarted everything. That is what bugs me. But just in case I missed something, I'll do it all again and will let you know.
I appreciate the quick responses. Thanks.