Hi,
Hormonal imbalance disturbs your health and the rhythm of your body. It can affect any normal functional be it your menstrual cycle, immunity, etc. One needs to get it checked and take measures to rectify it before it's late. Your problem seems of hormonal imbalance. I that case,you need to consult a Chiropractor and I would suggest Dr. Maegan Davis of Natural Body in Balance who is a Chiropractor for the last 25 years and offers natural ways of curing hormonal imbalance symptoms. Contact her at http://www.naturalbodyinbalance.com/ and let me know if my suggestion helped.
I don't know about your immune system, but your hormonal imbalance would cause blood clots, cramping, spotting, etc. It should not, however, cause flu-like symptoms or viral infections. Sounds unrelated - you need to get further testing from your doctor. Maybe your thyroid is out of whack (which can cause menstrual irregularities and a feeling of illness)