Have you tried a fresh re-install of titanium yet?
all the files that end in .s3d are going to contain "skins" as far as i know. the ones that say something_chr.s3d i would assume are mob textures for that zone. there are also global skins that are used in all zones, such as global_char. The ones that say something_obj.s3d I'm guessing are for objects in that zone, again there are global ones of these too. the ones that are just zonename.s3d are the actual zone
also as EQ client got older they started using .EQG to handle these textures instead of s3d.
my guess would be to look for the zonename_char.s3d files for the zones that have odd looking mobs (humans instead of dragons or w/e) and try replacing those.
As for the solid black appearance for epics and T8 weapons, really not sure what to replace there. gequip#.s3d maybe?
The staff or someone with more eq "hacking" knowledge can probably shed some more light on this. I know you're not the only one with this problem. I met others that had the same issue when I would ask about it in game.
You can download a program that lets you open and view the .bmp files that are embedded in each .s3d file. but a single .s3d file can contain hundreds of textures, it would take a long time to browse through them all but its worth taking a look at some of them to see what kind of textures they contain, ya know to see if you are on the right track. here is a link to the program,
http://www.eqemulator.org/forums/showthread.php?t=18203hope that ramble helps hehe, getting tired, been working all night, its my bedtime =)