It's not a complete answer, but yes there has been a drastic shift in hormones. There's a strong tendency to call any negative symptoms 'low-carb flu', just like people do with real flu, but I think that often misses the point. Low-carb flu is a combination of the wtihdrawal symptoms from being addicted to wheat and a more general systems crash while your body sorts out the hormone levels, enzymes, metabolic pathways etc. to get up to speed on a different fuel. If you've been functioning well for 3 weeks then that's not the issue.
There are a bunch of reasons why things seem to get harder. First off is the obvious one you mention. Your body and its needs change throughout the month. While I can't offer personal experience, if you eat the same food every day then you're logically going to be out of sync at some point in the cycle. You've got nutrients you need to replenish and a different hormonal environment. Feel free to experiment rather than thinking you must find one right way to eat all the time.
Speaking of those nutrients, you may just have run low on something which you regularly got in your diet before. Maybe you had a bad night's sleep or you've been exercising too much and you just need a break to get everything balanced again. Or maybe you're just not eating enough - regular carb-based diets tend to over-rev the engine, there's no risk of it cutting out. It's quite common on switching to lower-carb paleo to feel fine without eating as much. But sometimes the body needs a feast, and it's not a failure to eat more occasionally. Again, variety. A lot of people go back to reintroducing carbs. After a life-time of living on them they certainly can mask a multitude of ills, the ultimate comfort food. It's probably not the root cause of how you're feeling though. However you choose to tackle it, just remember it doesn't have to be all or nothing. It should be a constantly developing process of learning to listen to your body day by day.