Hi Chad
The 'knot' you describe will not go completly as this is where the bone has healed. I suspect the reason the 'knot' reduced is because any inflammation to the area will have gone down in your time resting from running and the area has inflammed again when you did your run after the rest period.
It is worth noting that stress fractures can take 4-8 weeks to heal and are normally caused by an acute change in training habits such as increasing the distance your running too quickly. I would advise seeing a Sports Therapist/Physiotherapist who can resolve any causes, biomechanical or otherwise, and take you through a well designed graduated rehab programme.
Hope this is of some help
Alex
[CENTER][I]Alex Dexter BSc (Hons) MSST
Graduate Sports Therapist[/I][/CENTER]