Sorry to hear that, it's never fun to have to wake up in the middle of the night and run to the toilet.
It may be caused by it's claimed anti-parasitic effect, which may have contributed to your nauseousness, but I'm not exactly sure.
During my OJ fast, I sneaked some coconut water from a young coconut one day, and the next day I had diarreah. After my fast, I drank the water and ate a few pieces of the flesh and had bad diarreah 2 hours later. A week later I drank the water and ate the whole coconut around 6pm, and felt extremely full the rest of the day, and couldn't eat my salad for dinner. I wasn't sick the next day though. I bought a mature coconut the other day and have been snacking on the meat with no problem and I also eat organic dehydrated coconut every other day. I made a delicious coconut oil/fudge with 1/2c coconut oil, 1/2c org. gd. B maple syrup, and 1/4c org. cocoa powder as a way to get a yummy dose of coconut oil everyday for its health benefits. I overdid it the other day and ate about 3 2x2" squares with no ill effects. I've come to the conclusion that maybe you have to build up a tolerance to some foods when introducing them into your diet.
I think the reason I felt so full the rest of the day after eating a whole coconut was because my body wasn't used to digesting it and so it kind of just sat there for a while until it figured out what to do with it.
I can't really say that I've seen any improvements from eating it but I can say that I am quite the "coco-nut." :)