The most common side effect of a Flu injection is minor soreness in your arm in the area where the shot was given. The soreness should only last a day or two.

You may experience other side effects such as fever, fatigue and body aches. These symptoms should also disappear in a day or two as well. If they don't, or you see a rash on your arm where the injection was administered, contact your doctor or healthcare professional.

Contrary to popular belief, receiving a Flu shot cannot give you a case of the Flu because the viruses in the injection aren't active.

If you came into my E.R. with the symptoms you just described, I would test you for Meningitis.
Symptoms of bacterial meningitis usually appear suddenly. Symptoms of viral meningitis may appear suddenly or develop gradually over a period of days. For example, the symptoms of viral meningitis after mumps may take several days or weeks to develop.

The most common symptoms of either form of meningitis include:

Fever.
Severe and persistent headache.
Stiff and painful neck, especially when trying to touch the chin to the chest.
Vomiting.
Confusion and decreased level of consciousness.
Seizures.
Other symptoms of meningitis include:

Sluggishness, muscle aches and weakness, and strange feelings (such as tingling) or weakness throughout the body.
Eye sensitivity and eye pain from bright lights.
Skin rash.
Dizzy spells.
The incubation period, the time from exposure to the infection to when the first symptoms develop, depends on the type of organism causing the infection.