<I've since changed my workouts to be 1 heavy lifting day (non-crossfit) every 5-6 days at the gym and WODs whenever they play to my strengths (usually 2-3 a week, but sometimes less).>

I've found this to work well for me also. I enjoy running and partaking in road races. I have come a long way in my evolution of training. I now understand that I used to over-train, and by a lot. I now lift close to the heaviest things I can about once a week, and perform crossfit-endurance workouts or my own metcon workouts I write up 2-3 of the other days or as I feel like doing. I meet up with 3-5 friends once a week at a park and we have a metcon throw down, which is good becuase nobody wants to come in last and it's friendly competition.

As for the original poster and his weight gain on the strict Paleo diet, I would love to see a 5-7 day food journal with rough serving size estimates. If you were to keep your carbohydrate level to 20-30% of your total calories, keep the majority of your carbohydrates to your post-workout meal, and do workouts such as crossfit WODs hard, I can't see one gaining body fat. Lean mass yes, but bodyfat no.

If you post a food log somewhere online I'm sure people here will take a look at it and give your their opinion / suggestions.