thanks for writing to HCM,
After reading your whole description it seems that your shoulder pain
is not related to your flu
This shoulder pain is due to muscles spasm (usually the trapezius muscle
). i would suggest you to start hot fomentation on your shoulder painful area 2 times a day for 15 mins with a hot water bag. and also start doing some stretching and strengthening exercises of your neck.
it is also important here for me to tell you if you are in a profession which requires long hour usage of computer kindly review your posture there. also start using a thin pillow while sleeping.
for the above mentioned exercises a physiotherapist can help you.
i hope this helps
wish you good health