Chaofanatic's model rips and stuff like that

So I've been ripping models from The Wonderful 101 lately but I'm not having much luck getting them actually uploaded cause I seem to be doing a lot wrong, so could I get some help with this?
I've been told my texture paths were wrong, the formats of the textures were wrong, my dae model didn't have rigging or texture mapping or anything and so on but I think I've gotten everything down now except for a few things. Blender's DAE exporter likes to connect bones that aren't supposed to be connected together and it messes up the orientation of things, and apparently my spec masks have something wrong with them but I'm not that sure what?

Would anyone be willing to help me out with this? The FBX file is perfect, but the DAE is the one with the problems
The Wonderful 101 - Commander Nelson

Also a lot of things in this game use alphatesting to show scrolling texture effects on them. Am I allowed to actually keep the alpha channel for the transparency in the color texture or do I have to make it separate? It doesn't seem like any alpha channel stuff is allowed here at all for some reason and it all has to be its own texture.