I'm guessing that you're too lean?
If that's the case there are a couple of things I would think may be affecting you. This would be more of a basic checklist. If you answer yes to any of these, move along below.
1) You are likely still in a state of over reaching or possibly overtrained.
2) You may have some lingering injuries that don't seem to get better.
3) You're cold all the time
4) Your sleep sucks, and you're probably moody.
5) Your, um, personal life ain't what it used to be.
again, this isn't medical advice, talk to your doctor, I'm not liable if you get worse:
Like you said, you likely would need plenty of rest. And food. If you are still pulling out from having uber low bodyfat, eat more, rest more. Make your rest active rest only to the point that it helps you. If it doesn't make you feel a little better in some way, it's not good.
One of the negatives that is being discussed in a mass gain thread right now is that so many people on a Paleo diet get so low on carbs relative to their activity levels that they get seriously jacked up. Carbs are inessential if you don't do much. if you like to be active and carry a decent volume of training, you'll have to reconcile with yourself to increase your intake.
For more information on how carbs can affect performance and possibly even health, check out this guy, if you can stand a little causticity:
You can also spend several hour, or even days, perusing Lyle's site, James Krieger's site etc.
Lastly, if you're concerned with issues pertaining to inflammation, you need to eat more plants.