From the description of your symptoms, especially the length of time that it has taken for the illness to resolve, and the ongoing fatigue and other lingering symptoms....
it is possible that you have a viral infection caused by EBV (which causes mononucleosis) or CMV. These viruses typically cause a prolonged lingering type of viral syndrome. Also, though not typical, both can cause a conjunctivitis (your eye symptoms). The symptoms are widely variable though, so it would be impossible to say for sure, without some blood tests being done.
Mononucleosis will usually clear on its own, taking several months sometimes for you to feel well again. The symptoms from CMV (cytomegalovirus) will usually clear also, but CMV stays with you, and you will run the risk of reactivation at a later date when your immune system is compromised because of another illness, or medications perhaps.
So, because you are still having symptoms, I think it is worth your time to see your doctor again and have some tests done to see if either of these is a possibility. There are complications that can develop for either type of infection in some people.
Here are some links for more information about these two infections:
Also, there is a possibility that you may have had strep throat. Normally (at least in the U.S.) when a patient sees a doctor for a sore throat, a throat swab is done to rule out a streptococcus infection (strep throat), since untreated it can also lead to complications.