Hammering up that hill right at the start of your ride can't be helping. I've got a pretty good incline at the start of one of my routes, I usually head away from it for a half mile or so before turning around so I end up hitting it with a mile's worth of movement under my belt. I don't know if this is physiologically sound, but it seems to work better than just hitting the hill cold.
I've been plagued by a nagging left knee on and off for years. A little bit of tweaking my position on the bike, a bit of working the muscles surrounding the knee, and a whole lot of stretching have worked wonders. If I stretch on a regular basis (at least three days a week, preferably every day), I find I have little trouble. Your line about taking on a more "demanding" stretching regimen pronto leads me to think you might be suffering from overexertion! There's an excellent book on stretching by Bob Anderson. It costs about $10 - $15 and is worth every penny.
Good luck.