Hmm, if you say that the mods don't work even in the normal unmodded game, then there is definitely something wrong with your setup.
Just to be sure, can you show me the following:
- index.html
- mods folder(also, is it called "mods" or "Mods"? that might be worth checking out)
- TY_ModLoader, specifically the "TY.MOD_LIST" section.