I have similar problems! Swollen tonsil on one side, also swollen lymph nodes on neck (much larger on side of swollen tonsil) and extreme tiredness and muscle aches! Also my hair has gotten a lot thinner! Been tested for nearly everything, had the tiredness, muscle aches and hair thinning for 8 months, and the tonsil and lymph node for 3 months now!
I would go back to the doctors and make sure the infection has cleared and not moved somewhere else.
Remember though that your tonsil may take months to go back to normal size after an infection (my left side is large than my right because of two infections within a month about 5 years ago). If the tonsil is not bright red, covered with pus or very sore, the infection may be from somewhere else in your body and the tonsil is enlarged because of the increased number of white blood cells in your lymph system.
Best to touch base with your doctor again and let them know it didn't help, they can't pin point the case unless you communicate back with them what works and what doesn't.
In the mean time, try not to be too stressed (I'm in my 4th year at university so I completely understand they will be a low level of constant stress no matter what you do), but do your best to keep it minimal. Drink lots of fruit juice for the vitamin C, try taking vitamin D and omega 3's to help your immune system and anti-inflammatory benefits and sleep and eat well. Gargling with listerine or scope a couple times a day may help too.
Hope it clears up soon, I know how hard it is to get over a illness during classes.