You seem to have had a particularly bad bout of viral infection.
Sometimes, viruses causing colds and flu can trigger an inflammatory response in the joints and this appears to be the case with you.
Symptoms are usually temporary and affect one or two joints.
However, occasionally, they can become more widespread. If the pain and swelling of your joints continue to trouble you, it would be best for you to see your doctor again.
To help resolution of symptoms, you may wish to use a topical pain-killing gel such as Atrogel®' Arnica Gel.
In addition, it might be worth looking at your diet too.