Ah yeah, that was one thing that went over my head... I completely forgot that whatever material you want to use on a character won't be used in-game until you define the texture set in a .upl file.
Easiest way to do this is to open up the .upl of the character you're skinning, edit the BodySkin and FaceSkin values so that they use your skin, give the character a name, then save that file to a NEW file (don't overwrite the .upl of the file you're editing!).
The format to use is PackageName.MaterialName
For example, if my texture package name is GoatTexturePackage, and the body texture I want to use in that package is Goat_Final_Material, I would type in that section this info:
BodySkin=GoatTexturePackage.Goat_Body
This ignores material grouping in the texture browser (it's just an organizational thing anyway). Then all you need to do is save the .upl as a new file with a logical name. In my case I'd probably save it as "Goat2k4.upl". The addition of "2k4" or "2004" at the end makes it easier to see at a glance if the file is meant for UT2k3 or UT2k4, or whatever version of UT comes next.
As for team colors, I think there's a tutorial on this forum already that can help with that:
http://forums.beyondunreal.com/showthread.php?t=141262
Your .upl should look like mine does below:
[Public]
Player=(DefaultName="Goat",Race="ThunderCrash",Mesh=HumanMaleA.MercMaleD,species=xGame.SPECIES_Merc,BodySkin=GoatTexturePackage.Goat_Body,FaceSkin=GoatTexturePackage.Goat_Head,Portrait=GoatTexturePackage.Goat_Portrait,Text=XGoat.Goat,Sex=Male,Menu="SP",Tactics=1.0,StrafingAbility=1.0,Accuracy=0.5,BotUse=1)
That should help, lemme know if that works.