I've been getting those clots for years, and I'm pretty sure I have endometriosis. I had really enlarged ovaries on ultrasound, but I did not want laporoscopy to get the definitive answer. I think the candida and liver congestion is a big part of that problem for me, and I'm expecting to see a reduction in those long, clumpy periods after an extended period of time on the BED diet and more liver flushes. I have heard that some women experience a lot of improvement in that department with the flushes.
As for the fatigue, yeah, that sounds like a cleansing crisis. It's a process - none of this stuff happens overnight. It took you years to accumulate enough toxins to make you chronically ill, so it will take awhile to get your health back to optimal. Just rest as much as you can and take care of yourself, and work in some kind of exercise daily, even if it's just some stretching or gentle yoga, or a short walk.