Firstly nice one on going apocalyptic! I absolutley LOVE huuuge armies!!!
In respect to colours for the forces, I would personally pick a chaos god/ force first (Slanneshi, nurgle, chaos, Tzeench/ Black leigion, red corsairs ect.) and then this would dictate your colourscheme (to a certain extent anyways, I am also a big fan of the \' its your army paint it whatever colour you want!\'school of thought!) and then I would use that colour on the guard also to help tie the force together.
In respect to your colour blindness, are there any colours that give you more jip than others? (I have a mate who is colourblind and struggles differentiating when painting with reds, greens and sometimes browns). Also if you have a whopping 5000 points to plow through you may want to stick to a scheme in your comfort zone that you know you can do quickly and easily.
Hope this has helped cheif, and remember to keep us posted on progress with lots of pictures!!!