Well, each one of those needs their own explanation.

For paintable textures: You need a texture made with the part you want to be painted white (with just the AO map), and in the alpha channel of that texture, you need to paint white the part you want to be painted, and black the rest of the texture. Then in the importer, you check "Paint VMTs" and in the vmt editor, you will have to set the RGB values for the default color.
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Team colored textures: You just need to make 2 versions of the texture, one for blu and the other one for red. In the importer, where it says skins, instead of "All Team" choose "Specific team". Then you'll be able to choose a texture file for RED and another one for BLU (and they can be paintable, just do the same as above)

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Shiny textures: If you aren't going to make the item paintable, just paint the alpha channel with white on the parts you want shiny, and in the VMt editor in the importer, check the "Base map alpha phong" and adjust the "Phong boost" option so it shines as you want.
If the item is paintable, you'll already have an alpha channel (in case only some parts are paintable). Then, you need a plain normal map (max 256x256 pixels) with an alpha channel painted the same way you would paint it in the original texture for the phong. Again in the importer, go to the VMT editor and load the normal map into "shared normal", uncheck the "Base map alpha phong" option, and adjust the "Phong Boost" option to your like.
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Aside from that, i don't know how to make transparent textures, but i hope all the walltext i wrote helps you ^-^
And if you don'tunderstand something, feel free to ask