Well, if you did your own preliminar fit, it is time to tweak it based on how you feel. You don't mention if you are using clipless pedals, but if you do, those can be a source of knee problems even when the rest of elements are roughly well fitted. From experience, I have noticed that people doing their own fit tend to have the seatpost a tad high, because this is something that gets remarked a lot and in making sure it is high enough we usually overdo it, if just for a little.
So, a centimetre or even less of adjustment of the seat height or sliding it forward or backwards in the rail, can make the difference between pain / discomfort or a pain free ride.
Go for a ride with your tools and see how slight modifications affect your riding, but it is an ongoing experience, since even with a professional fit you may need tweaking, more so with your own fit. I kind of start listening to my body and have changed my cleat position like 6 or 7 times in a year, always getting a bit better. Saddle tilt is also something to pay attention to. All in all, if you don't want to go for a pro fitting session, experiment and note down what your body says in order to make or keep changes. Again, even a slightest tune up can make up for a change you wouldn't imagine.
Remember that easier gearing is also easier on the knees, pedalling cadences of around 90 are recommended, and having good support muscles will also help your knee so work them a bit, like walking upstairs, riding other bikes without cleats.. there are many exercises for strengthening the knee area, even dreaded squats.
Experiment, don't take the first fit as the definitive fit !