I am just recovering from the flu and I can relate to the stuff you experienced.
Here is what happened with me:
Since December I have had bouts of feeling cold, sometimes I was even shivering under two blankets while it was 22 degrees (C) in my room. I thought it was TMS, so I tried to approach it that way. I also suffer from mild hives since then, which imo is due to emotional stress (my doctor also encouraged me to approach it that way, which was awesome in a way to hear a doctor acknowledge that it is often the main driver of hives)
Then last Tuesday I started to shiver so hard it hurt really bad in my abdominal and back muscles; a couple of hours later I had a fever and only today I feel the worst is over. I had a slight runny nose and sore throat, but not like when you have a real cold, the main problem was a high fever, sore muscles and sleeping 20 hours a day.
Eating something digestible like a banana can really make a difference. Find a site about the flu and you will find that it is encouraged to try to eat things like.... banana's... I also ate pieces of toast with honey, which somehow made me feel better too.
My theory is that I didn't allow myself to get sick for close to two months. The mild case of hives tells me I was 'TMS'ing' and therefore I was spending my time in survival mode. It is possible to postpone a viral infection via survival mode, which is why many people get sick once their weekend or vacation starts. Just ask around and I bet many people will concur with this. Too much emotional stress can also trigger getting sick, which sounds like a contradiction, but the body can only take and postpone it to a certain extent. So where stress can postpone, too much of it or a sudden lack of it can trigger a (healthy) reaction where the body will deal with the virus once and for all (and build immunity so you won't get sick a second time... that's why I advise you to allow yourself the time to get better).
As I somehow foolishly tried to gain control over feeling cold by meditating and allowing any emotions to be there, I noticed that allowing the sensations only made them worse. In retrospect it somehow makes sense as I temporarily opened the gate for my body to deal with the virus in my body once and for all... I still have the hives, although I really couldn't care less. I bet it will go away sooner than later.
If the above doesn't make sense, it probably is because I am still not 100%

I am also interested in any other ideas on how the flu is related to TMS. Maybe one of the authors of TMS literature wrote about this, but I still feel too tired to dig into that. The only thing I remember reading is that 'staying at home with a cold is the western way of meditation'....
just give it a couple of days, drink plenty of water to stay hydrated and take some paracetamols to counter the worst and help to get some sleep (
acetaminophen, in my mind one of the few legitimate drugs you should take when you have the flu).
to your health!