This appears to be too complex to handle through this forum alone. I think we could work this out in a 1 hour premium support ticket if you are interested.
I still don't fully understand how your discounts work. Would they apply across color and size selections, or is the qty only applicable for the current size and color?
If we insert the discount amounts with the cart, then if they change the quantity afterward then the discount may become inaccurate. I'll need to fully discuss this with you and probably use some custom code on the cart page to get it all working the way you need it to.