Ben, in my experience, brain fog is related to digestive health. I'll guess that you had some traveler's diarrhea in Haiti perhaps? Or at least some digestive disturbance, and maybe now you still are having issues. You say you "had the runs" as if that was related to your consumption of non-paleo foods, but I'd imagine it is more complicated than that and is related to your now compromised digestion.

Look into either the SCD diet or the GAPS diet. I had debilitating brain fog a couple months ago. I've been on the SCD since January and have made striking improvements. The bacteria in your gut, it seems, can cause disturbances in brain function (I have no references for this - completely anecdotal). Feel free to comment if you have any questions or need help on the diet.

With the trip overseas being part of the equation, I'd think you should consider the possibility of a parasite or other organism being a trigger. Even if it is gone now it could have left the body "rippling" with aftereffects.

It's a great question and I hope someone can provide a well-researched answer. I've been trying to make sense of the inflammation/gut permeability connection with brain fog. The best I can figure is that the blood brain barrier gets compromised, or you otherwise have inflammation (i.e. pro-inflammatory interleukins, NF-kappa-B, etc.) within the brain, and that causes decreased efficiency of neural signaling some way or another. NF-kappa-B, a transcription factor, regulates gene transcription for genes related to neural signaling as well as inflammation, so maybe that is one possibility to explore. I used to work as a research technician in a stroke lab doing proteomics-type work, but I haven't heard of anyone looking at the role of neural inflammation outside the context of ischemia.

Another possible connection is via serotonin production in the gut. I've read (on non-academic websites) that a lot of the body's serotonin is made in the gut, but I haven't seen anything on whether that serotonin stays in the gut or crosses the blood-brain barrier to affect neural signaling. But that could be a second mechanism by which a person suffering poor gut health could experience sweeping cognitive changes.

Brain fog = not enough carbs....Up the carbs a bit, maybe add in a sweet potato and see how you feel. I would expect some improvement!

I do not know what the main causes of brain fog are for everyone, but can write a bit about what helped get rid of some brain fog, for me.

Some things that have helped me:

Diet related:

Eating a ketogenic food plan. Also, making sure that what I eat is nourishing. I don't eat things that could cause troubles.

Avoiding packaged/processed foods, with all their additives, preservatives and mystery ingredients. The FailSafe diet helped with this.

Avoiding: grains, legumes, nuts/seeds/their oils, nightshades, oxalates, salicylates (except black or brown tea), goitrogens, FODMAPs, sweet fruits.

Following Dr. Richard Bernstein's Law of Small Numbers, which means eating constant amounts of CHO and PRO from breakfast to breakfast, lunch to lunch, and supper to supper, day to day. And, eating small amounts at time. Small meals. This keeps blood sugar normal and stable, for me. Constant blood sugar means clearer thinking. Eating too much protein, at one time, or in one day, makes me feel unwell and out of sorts a bit later.

Taking supplements: magnesium, L-carnitine, CLO with a dab of butter, Vit. D and E, nutritional and brewer's yeast, PicMins minerals, for a few examples.

Drinking tea helps me. Too much tea causes troubles. As with the other things, it takes experimenting to discern how much, how often....

Non-food aspects:

Getting proper rest and sleep.

Doing yoga, Callanetics, rebounding, taking walks. Calming, strengthening, and restorative, for me. Callanetics combines yoga with ballet training. Yoga is known to increase GABA.

Balancing rest and exertion, being alone and being with others, work and play, etc. Easier said than done, I know. :)

Avoiding things/people/situations which are, for me, too much input at once. I don't go to the cinema. I avoid crowds. Don't listen to the radio very much. I like being around folks who are circumspect and value quiet decency. I like being able to hear myself think. :) This aspect of being able to think clearly takes deliberate care nowadays. Before television, every day life was much saner.

Those are the things which come to mind, at the moment. :)

Hope they help someone.

It's too complex to pin it down to one cause, one solution.

I have experienced it due to three reasons. 1. Poor sleep. I have sleep apnea and still use a machine. Fixed. 2. Eating too many simple sugars, before I knew better. 3. Wrecked thyroid, complicated by insulin resistance. The fix was meds and VLC.

for me--

aldosterone issues with hypotension
thyroid exacerbated by vlc. 

i eat more carbs now but i'm still not myself

Here's a link that suggests many causes for brain fog: http://naturopathconnect.com/articles/brain-fog/. Anyone with protracted brain fog should probably be tested for Lyme disease and its co-infections. These infections can produce quinolinic acid, a neurotoxin, which Great Plains Laborabory has a test for as well as information about how to manage at: http://www.greatplainslaboratory.com/home/eng/brochures/Toxic%20Chemicals%20Brochure.pdf. The herbal supplement pinella, which is part of the Cowden protocol for Lyme disease, can help. Agree that leaky gut can also be a cause and SCD diet (or GAPS or low fructose) may help. Look into SIBO (small intestinal bacterial overgrowth). There is a Yahoo discussion group dedicated to this topic. It can be diagnosed with the hydrogen breath test. Chronic fatigue syndrome and mold intolerance can also play into brain fog. That said, I have brain fog and have not been able to quell it. I also have Lyme disease that has been treated as well as SIBO, which is currently flaring, and CFS. My brain fog has come on two years in a row in December so I thought it may have been light related; however, it is mid-May, and I still have it this year. So much for that theory. Yesterday, I took some colostrom, and it seemed to help, but I don't know if that will hold. If anyone finds anything that works, please post.

Brain fog is from mold. All Paleo foods are low mold food. People think its sugar but its only because sugar is in most moldy food because it feeds mold.