"my knee has been swollen for quite some time now (3 months) and it hasnt gone down much at all yet" - I would strongly reccomend seing a doctor if it's still as swolen as you said it was.
I have and i have gotten an MRI too. they just said that it was a lot of internal swelling.
I had one of those last time I hurt my knee (got kicked in the knee though, not free running related).
I tore the cartilidge disc the knee sits on, almost had to have surgury, if it had torn any further it couldent have healed on its own.
If the knee swells and locks up, see a doc.