Thanks again everyone for your responses.

The pain is all around the kneecaps (that's how I can best describe it); it sort of comes and goes. Yesterday (Tuesday), I had a tough commute (first time I had to go out of the city, round trip, into the countryside) so I was scared because I had pain the night before, however I'm not having pain right now (Wednesday) even though I rode today as well. As of the past two or three weeks I haven't even touched the last 3 upper shifts -I think-, so that may or may not be why I'm not having worst pains now, I'm guessing it's a cumulative thing, right?

About the saddle, it's already all the way back on the seat post, and about two weeks ago also I raised it almost to the same height of the stem, I don't want to raise it further I think, because it becomes uncomfortable when I'm pedaling 'outside' of the saddle, or 'standing on the pedals', if you will (it gets in the way of the inside part of the legs).

I don't have wide feet, do I still benefit from pedal extenders? As in having the legs spread apart a little further improves posture?

One thing I've been wondering for a good while now is if I could benefit from "wider" platform pedals (wider front to back, not side to side) so I can have a larger portion of the feet in contact with the pedals, transferring movement. My bike still has the stock plastic pedals but I don't really know what pedals to upgrade to. Btw I use this Shimano shoes with the option for cleats, I'm not sure I'd feel very safe 'locking' myself to some pedals though. But maybe it could help with the feet posturing? I don't know if using something with toe clips would be better for me, because my feet keep moving all over the pedals (specially with rain or moisture).. Or I guess maybe having the feet changing position on top of the pedals is better for relieving stress from the knees?

Any suggestion for pedals? Don't really know what to look for.