Would I suggest you eat non-Primal foods? Nope. There's no reason you can't count calories and eat Paleo/Primal - I sure do. Once you've gotten some healthier eating habits, ie, knowing how much you need to eat, you can stop. This is like... let's think of it as training wheels.
Let me give you some advice on calories. This is my take.
Now, I don't know your BMR, TDEE or whatever. But this is how you start:
1g protein per lb of bodyweight.
0.5g fat per lb bodyweight.
In my case, that's 121g protein (484kcal) and 55g fat (495kcal). These are MINIMUM.
Now, my BMR is 1400 something, my TDEE is 2000 - but I'm eating 22-2400 to gain. So, to calculate:
=1221 remaining calories.
Those remaining calories you can fill with ANYTHING. Carbs, fats, protein - whatever you like. Want a sweet potato? Eat up! More bacon? Go for it! So long as you get minimum protein and fat requirements, fill the rest of our remaining calories wth whatever.
Just remember to fill them.
Work out things for you the same way. Ignore MFP's calories suggestions; they're generally to extreme. Set yourself to lightly active at least (at LEAST), then deduct 10-20% off that and set that number as your goal to lose weight.
This, IMO, is the best way to go about anything. Weight loss or gain - I'm doing the very same thing, just in reverse.
Hope that this helps.