Runech, I see you posted this half a year ago so my advice may be coming too late to do any good. There is a lot of advice available from riders and many have had knee pain and can tell you what worked for them, but I suggest you only use the advice of a professional that has examined you. Don’t be your own doctor, and don’t expect any dietary supplements, particular exercise or corrective devices to do you any good (don’t go out and get a knee brace!!!!) unless they are indicated by a pro that knows what’s wrong with you.
The good news is that the great majority of cycling knee injuries can be treated and fixed, and the diagnostic powers and rehabilitative methods in use currently are quite advanced and effective (It’s a great time to have a knee injury). While it’s possible that you may have “damaged” something by doing 1000 Km with a bad fit, it’s not likely. Surgery? Almost never indicated in cycling related knee pain. Biking just isn’t associated with traumatic injuries in the way that running and other impact sports are.
Seek a professional who SPECIALIZES IN SPORTS INJURIES, AND SPECIFICALLY CYCLING if you can find one. Don’t waste your time or money on one who doesn’t specialize. This would be a physical therapist, medical doctor, certified trainer, or similar professional with expertise on cycling. Again, the more specific to biking he/she is the more value you will get. If this person isn’t also a bike fitting specialist, find one and get an exacting fit based on his detailed analysis of your body and bike.
Should get you all fixed up and riding in no time.