Don't worry about your 6:3 ratio if you're following strict paleo. The people that usually have to worry are those eating typical crap.
I find whey to be no problem because it isn't acid causing like casein is and has very low incidence of allergy.
Most people eating paleo forget to get the monounsaturated oils. I still like to shoot for 1/3 saturated, 1/3 poly, 1/3 mono. I use macadamia nuts to keep this balance. They are also basic on the PRAL scores.
Just eat whole, unprocessed foods and supplement with fish oil. If you're trying lose bodyfat, keep fruits minimal and tubers to post workout. If you're maintaining, you can loosen it up a little. Always eat lots of veggies and greens. Eat when you're hungry and get obsessed with measuring food.