I agree with Starfish. I think that the best thing to do right now would be to take a couple of weeks totally off from any activity while doing RICE and possibly taking some anti-inflamitories. This will give the knee a chance to recover from whatever it bothering it. It is possible that you have tendonitis, but it can be really hard to know what caused it initially, and what just aggrevated it once it was started.

After your knee has calmed down and you start to slowly add activities back in, I would go back to the LBS and talk to them about your knee and have them look at your pedals. you may want to pay for a professional fit with someone who is experienced with these things. Tell them about how your knee felt when it hurt, how your knee used to turn out when you stood before getting clipless pedals and how it doesn't anymore. It seems possible that if your knee wants to rotate out and with the new pedals you don't let it do that, that could cause some stress to the knee. I am not a Doctor, but mechanically that makes sense. It might be that you have to switch to a different kind of pedals that allow your knee to do what it would like, maybe something with a lot of float like Speedplay zeros.

Good luck! I hope your knee feels better soon and you are back on the road!