Christ, I have had some nasty injuries over the years, but the fibula stress fracture was the worst without question. Does it hurt to put pressure on the lateral side of your lower leg while pushing with your palm? If it is extremely sensitive, you probably have a fracture.
The strange thing about a fibula stress fracture is that it is not a weight-bearing bone, and the fracture is not caused by impact induced stress like most other running fractures are. Additionally, you may be able to continue running for some time before it gets really terrible, at which point walking will become very painful. Furthermore, the fracture probably will not show up on an x-ray until later (for some reason, ask a doctor).
My fracture seemed to be caused by too many miles and tightness in my hip and lower leg muscles that began to torque on the fibula. I trashed the thing really bad, and it took about 8 months before I could get back to running slowly. During this time I found stretching the peroneal area to be comforting. It is difficult to describe how to stretch the area, but if you plant your foot and invert your toe while doing a lunge-of-sorts to stretch the tendon running down the side of your lower leg, you may find that it relives the feeling of fatigue that you described.
The bottom line is that you need to rest, rest, rest.