Milkshape 3D is a good ideia if you only want to change the weapon, since its just a md3 file, you can easily import and export, but you have to create a qc file to export.
I don’t know if it is necessary to create a new mdm (the file for the body) or a mdx (the animations), but a program that may work is the Lightray 3D, it can import and export mdm/mdx, but never used since you have to pay for it xD
Here is a idea what a qc looks like:
// Quake III Arena MD3 control file, generated by MilkShape 3D
//
$model “models/players/model/model.md3” <- Edit this
// reference frame
//$frames -1 -1
// frame 1-30
$frames 1 30
$flags 0
$numskins 0
// you can have one or no parent tag
// tags
// meshes (surfaces)
$mesh “helmet”
$skin “models/players/model/skin.tga” <- Edit this
$flags 0
$mesh “inside”
$skin “models/players/model/skin.tga” <- Edit this
$flags 0
$mesh “strap”
$skin “models/players/model/skin.tga” <- Edit this
$flags 0
You can generate it easily from Milkshape, just go Tools -> Quake III Arena -> Generate Control File
As you can see, this the helmet qc, but you have to set the exactly path where the textures are and the md3. Also, you have the create the qc with the same name of the md3 file that you will create.
About the scripts, I’ve never did such thing, but you can try see the TCE mod.
If you want some help on Milkshape I would be glad to help ^^
Regards,
Rampag3