I unfortunatly have been in the same bike seat as you!
I bought a bike three years ago, my first real bike and didn't know exactly how it would feel and like you it never felt right. I was always having problems here and there.
My husband has become a techno bike guy in three years and realized it wasn't me but my bike, it was to big for me and my reach was way out there. He built me a new one. I was going to sell my other bike, but decided to keep it for when people come to visit. We live in a great biking town so it made sence to keep it. But maybe sence your bike is not that old you could sell it and buy a new one.
I also noticed that the more I bike the less my knee's (which I have problems with too) bother me these days. They bother me more when I don't bike.
Blessed are the flexible, for they shall not be bent out of shape.
> Remember to appreciate all the different people in your life!