I came across this problem and it took me awhile to fix it. since i couldn't find i guide on how to do this anywhere i decided to make it to help anybody else that comes across this same problem.
So you have a brres file that you got from another game like New Super Mario Bros Wii for example. lets say you want teresa (boo) and you run Fortwaffles's mdl0headerfix. so you open your brres and you find this:
Oh noes it only did one mdl0!! now your probably thinking you did some thing wrong but in fact you didn't.
Fortwaffles's programs only work for the first mdl0 it sees. in this case it would be fog. The answer to fixing this is quite simple. first get your brres and open it with your hex editor. Then search for the first string of text that says MDL0
now you see that string of text that says Mdl0? change the 0 to another number like 2. it should now look like this
now save and exit the hex editor and run the mdl0headerfix on the brres file again. you should now have this
yay the second model is there but what happened to first one?!?
Remember that 0 you changed into a 2? well open your hex editor again and change the 2 back into a 0.
now save and open your brres in brawl box.
TADA! now you fixed both mdl0's headers! as you can see there are four more mdl0 files that need fixing and fixing them is essentially the same as what you did for the seconded one. just find the first string of text that says mdl0 and change the 0 into a 2 like how you normally would but instead of save and exiting you go to the seconded string of text that says mdl0 and change that 0 into a 2. then you would follow the rest as usual.
to fix the materials and polygons you need to use the original hex guide.
hope this helped!
if you have any questions feel free to ask.
<-DemonBoy->