Ruxith

Basically, in a team game you either need model_blue.skin/model_red.skin files, or your skin needs to have RGB and be inside a folder starting with "jedi_<name>" if you want team colours to work; the "jedi_<name>" solution is only for RGB skins, and the team skin files are for non-RGB skins.
 
You don't necessarily need head/torso/lower .skin files/species support or for it to be inside "jedi_<name>" for working RGB in team modes. Actually, if your skin just has rgb and you don't have species support then the RGB will automatically change, it doesn't need to be in "jedi_<name>" folder if I remember correctly, it only does if you have species support. I was testing this myself not long ago.
 
Your texture needs to work from 2 separate images  if you are using transparency. The solution I found is located here. If you have any problems let me know.

Ah I didn't know that, worth noting thanks. I presumed the alphaFunc was how chewbacca's shader looked, I don't know why I assumed that but I just checked and I was wrong
I tried your suggestion but it didn't help, here's an image reel of the shader outcomes, i'm almost there with using the shader for the chewbacca (just a change in the blendFunc's in comparison to your shader suggestion) except it RGBs the whole visible area of the texture:

 
The image used was the same one I posted above, when I add a layer transparency mask to the RGB area of the image, it simply reverts to the first result, where the RGB area is transparent.
(sorry for spelling your name wrong I rushed the pic!)
 
Edit:
Fixed it, although your shader didn't fix it, it put me in the right direction, thanks man.
 

 
For anyone else who wants to look into making a model part that has transparency and making it RGB'd, here's my shader file:
 
 
 
Basically you need your transparent image as the main texture, then you map your RGB file (only your RGB area visible in the image) and that's where the "lower6b" will go in the shader file. No fancy pngs with layer transparency masks are needed.

Apologies for the double post, but I have fixed my shader finally!
 
 
It includes: 2 glow shaders, 2 RGB shaders, 1 spec shader.
I looked back at the first RGB tutorial that I looked at when I begun trying to figure out how it was done, back on jk3files, again by Crazy Assassin (big credits go to this guy!).
Thankyou Inyri and Milamber for the help you have given to me during this, and i'm gllad I have managed to finally figure it out with your help and the tutorials.