mmm as I already said, I already converted both 3ds and obj without problems using 3dexp.
Example: the xwaup ships can be converted from opt to uvmapped 3ds, and they use dozens and dozens of different small textures (some ships have 40+ textures...), and I never had any problem opening them with truespace directly and saving the uvcoords, and I never noticed this splitting verts thing.
also, I used 3dexp in the past to convert both 3ds and obj to cob, IIRC saving the uvs for obj too.
And flipping faces in TS is pretty easy, but unfourtunately there isn't a merge verts tool
BTW, if someone can solve your problem, it is probably nico