If you haven't done it in a long while, I would suggest getting a blood test to check some health markers and see if you can glean any clues as to why you became so ill.
One thing I would check is vitamin D level, which is commonly low in modern societies and that can contribute to infection susceptibility. My own vitamin D level fell to a very low level on raw Paleo, which I had no way of knowing until it was tested, and I was able to get it up to within the normal range on my last test. I'm not saying that applies to anyone else, just that it's good to get some objective tests of health markers now and then, because there can be hidden issues one doesn't know about, even when one feels great.
Another test to consider is a comprehensive metabolic panel. I've noticed that VLCers tend to have some suboptimal results on that test--and I had some out-of-range results on a metabolic panel when I was VLC Paleo (all since normalized after diversifying my diet).
I'm not trying to imply that tests are the be-all and end-all, just that they can sometimes provide some clues. Good luck!