Only way to know for sure if you have a stress fracture in the early stages is to do a bone scan. X-Rays won't show anything for several weeks.
Sounds like a stress fracture to me (I base this on having 3 different stress fractures before). Do you feel sharp pain in one localized spot? If you keep running on it, you'll keep messing it up. If you let it rest for 3-4 days to let the healing process start, then go run on it you're just going to set yourself back. Just because your foot feels better after 3 days, it does not mean it is healed.
I'd have to reference "Lore of Running" by Tim Noakes to verify, but in a nutshell the only way to cure this is complete rest of the foot for several weeks (at least 4 weeks). It sucks, it'll set you back, but to heal a true stress fracture this is the only way to do it.
Go to the library and check-out the book. It has a very informative section on stress fractures (among many other injuries). Or just buy the darn thing, it is a useful reference.