I don’t rebuild TQ models, I use mesh converter (change 4th byte of file), that mean all links to shaders, textures, mif data stay same.
GD have not shaders/foliaget.ssh file and i replace it by shaders/effects/foliage.ssh - copy, rename and put it in needed place, then build new shaders.arc.
As you say “…it uses to fade out objects when the transparency call is made.”, transparency call uses <shadername>T.ssh instead of <shadername>.ssh
As far as I use shader named foliageT, game trying to find foliageTT file for transparency. That was final solution. I actualy not use T shader for the base model, I use shader that names as T.
Swapping them out worked. Custom model rebuild with 3d max, proper hitbox and proper shader links worked. I was only not sure about hitbox name.