Have you read the free eBook Primal Blueprint Fitness?
Primal doesn't advocate a ton of running at the 80-90% MHR level which is where most runners are at. That's where I was. Instead, try to do the bulk of your activity in the 55-75% MHR range and then do strength/resistance training 2x/week (this is referred to as "Lift Heavy Things" or LHT around here) and then do a series of all out Sprints 1x/week. Go at MAX effort for 30 seconds or so, then rest until your breathing returns to normal, repeat 6-8 times.
If you are still trying to do a ton of running at that 80-90% level and your carb intake has lowered because by cutting grains and sugars they are naturally going to lower, then you either need to:
1) Stop running and do more walks/hikes/low level stuff. Why are you running? Is it something you enjoy? Are you doing it because you think that's what you have to do to "be healthy"? If you don't like it, stop! And then do things as described in PBF.
2) If you (like me) are running because it's something you enjoy, then SLOW DOWN. I went from running every run as hard as I could to doing almost all of my runs at a slow enough pace that I'm right at the top edge of the 55-75% MHR range. It took a little getting used to, but now my runs are much more relaxing, stress relieving and enjoyable than before -- I finish more refreshed than dead. I also do fewer of my old style long-distance runs and have substituted in weight training and the sprints I describe above in their place. I also just plain old walk a lot more, too.
3) Even if you are slowing down, a lot of this type of running means you are probably going to need to take in more carbs than a person otherwise would need. Starchy vegetables and tubers as well as white rice are good sources that don't have grains and other anti-nutrients. Try to take in your "safe carbs" immediately after your run as that's when your cells are most insulin sensitive and the spike in blood sugar will cause muscle glycogen to be replenished (which if it's not will lead to feeling tired on subsequent runs) and not promote fat storage.
Here's a couple of articles Mark wrote on how to train and fuel for a Marathon. Even if you aren't thinking about a marathon, a lot of the strategies are appropriate:
-Train low, race high
-Up carb consumption, especially immediately after a run.
How to Train for a Marathon | Mark's Daily Apple
How to Fuel a Marathon | Mark's Daily Apple
Mark makes no bones about it that he doesn't think lots of long distance/endurance running is the most optimal way to go from a fitness standpoint, but that he recognizes that people still like to do it. Here's an article where he talks about ways people can do these kinds of activities and minimize potential issues:
Primal Compromises for Athletes | Mark's Daily Apple
Other than that, I need to know a little bit more about what your goals are. Do you want to long distance run because you enjoy doing it? Or, are you just looking for best way to get fit? I've made a few assumption here and really don't want to give anymore advice until I know for sure more details.