sounds like you're doing pretty good so far. when it comes to muscle, you've got to consider your goals: do you want to look strong, or be strong? if you prefer the bruce lee look, you want to keep working on losing body fat. but, that will come mostly from food, sprinting, and explosive lifting (body weight or at-home work is just fine). losing the last bit of body fat is hard, and it takes time. keep eating primal, moving slow, definitely add sprints if you aren't sprinting, and consider programs like mark's Primal Blueprint Fitness or Simplefit, plus adding some explosive work on top.
increasing your carb intake is good for a couple reasons, specifically increased energy and increased muscle mass (by increasing glycogen stores). having potato every now and then isn't a bad thing...just keep your carbs primal (no grains, legumes, etc.) and keep moving.
your running seems okay to me. a few miles a few times a week isn't chronic cardio. there are people on these forums who use 3 miles as a warm up, and people who use 3 miles as a goal to reach one day...it all depends on your own comfort and fitness levels. but try replacing your boring run with a little persistence hunting for a better workout. rather than cutting back on the running, just add some lifting and sprinting and any other exercise that lets you reach whatever physical goals you may have