You should probably go see a sports specialist rather than relying on the internet, but here are some resources to help you figure it out. Common knee problemsPatellar TendonitisPFPS (Runner's knee)
Thanks Micheal, none of those seemed to match what was going on with me, but it wasn't a very big deal. I'm pretty sure that in a few weeks it will be gone after my body is a little stronger. I'll be careful though :)
A bit of rest and then a specific strength routine building over months should be the cure. Be careful about jumping into shorter faster races, it produces greater strain throughout your legs.
Those 400s will be tough, cut back the pace a bit and do more of them (as intervals), would be my recommendation.
I'll do that. I should be moving more into the 800 and mile over the next couple of weeks and hopefully that will give it enough time to recover.