Quick question:

If I'm going slow and I hit the brakes hard, I hear a kind of light 'thunk' from the front as the suspension compresses.It also sometimes does this going over bumps. It doesn't do this all the time, however.

I also noticed that the middle bolt cover on the steering stem (the one you see when you look straight down between the clipons) comes out a little over the course of riding. It's a little loose, but I don't think it should be doing this.

What should I get looked at?

 

i would say that you need to tighten it man that sound you are hearing is your front eend triple clamp clunkin around most likely if it gets that loose to hear a sound you need new bearings and possibly new races. there are special tools to tighten that stuff down. get it back up to torque specs