Just thought that I would throw in my two cents here.
It seems to me that if the mtl file is set up right everything should load right. -
I haven't fully tested this yetHowever, if you have to manually set up the textures like you have mentioned, be sure to export the model to .tgo and you won't need to do it over using the new file.
note: this will also work with objs that don't have a mtl file. if you have the original textures just manually add a default shader to the multi shader of the object. Do this for each texture you have, adding the texture as the color image or alpha where appropriate. If you are able (obj are not very stable in TG2tp) be sure to do a render to make sure you got the textures into the right shader slot. other wise export to tgo and then render to see if the tex. are right.
This is a very basic explanation and I'm sure I confused a few people there but perhaps it might help somebody