You should definitely read Famine's hybrid guide. The color cannot be altered much.
Thanks to MK's program, you can choose among available colors.
Suppose you want to change the color of your RX-7 LM Race Car, it'll be silver, blue, red, green or black and that's all. You can't have it painted green and orange like the 787B.
When you edit the .ini file (that MK's can generate), you can also 'supershine' it so that it has a chrome effect (like in WRC 2) on top of the chosen color.
Now you can do searches on all this : hybrid guide, MK...