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I know I'm a raving hypochondriac but this is getting silly.
I had a virus with all of your first set of symptoms a couple of weeks ago - it really knocked me sideways and I still don't feel 100%. So take it easy. Agree that you should get the thyroid thing checked again.
I couldn't not write after reading this, as I have days like that as well.
As for the throat and mouth issues, perhaps have your GP check your tonsils? I had the same type of thing, swollen glands, sore throat, ear aches and headaches, plus just a general run-down feeling that lasted for months. I ended up seeing a few different doctors who just passed it off as a virus, and then a bacterial infection and prescribed anti-b's. I finally made it to a Ear, Nose and Throat doctor who took out my tonsils (yes, even at 23 they take out tonsils) and I have to say that I felt about 100 times better once the surgery site had healed.
Perhaps you're cold because of poor circulation?
Sorry I can't offer the answer or solve anything but hopefully you start to feel better soon!
PCOS? - weight issues, generally feeling like shite and ovary pain followed by period pain.
Echinacea and plenty of foods containing garlic, tomatoes, broccoli etc. (superfoods)
(sorry, stubborn verrucas made me rofl! )
Have you been to the dentist lately and had your teeth properly cleaned? Sometimes mouth ulcers, recurrent sore throats etc can be from teeth.
Are you anaemic? (tiredness and menstruation issues). If not, how much exercise do you get? If you are knackered on your days off and there is no medical reason then can you get out for a walk/swim? Lack of exercise can make you feel very tired and lethargic.
Haemorroids - really common. get some cream and take paracetomol if sore.