mild pain/ dark spot, possible bruise on top of foot lasting over a year

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I became a runner in 2009 (started as a beginner and worked up to 5k, completed several races of that distance, etc) and then became pregnant. I quit running for awhile, and had some foot pain throughout the pregnancy but attributed it to weight gain and differing center of balance/posture. I did notice a dark spot on the top of my foot, but never thought of it as a "bruise" until last week when I sought treatment for the first time (over a year later) because I wanted to start running again. There is no constant pain, but it comes and goes (especially when I'm on my feet for extended periods of time, etc). My doctor suspected a stress fracture, and sent me for x-rays but they came back showing no fracture, no mass, no excess fluid, etc. There is some minor swelling in that foot as well.
Mostly, I am wondering what else could be causing this. I was prescribed an anti-inflammatory medication to be taken for the week to see if I have improvement, but I honestly have not seen any change except that the swelling seems to be reduced. Pain comes and goes, the "bruise" is still there, and running or being on my feet too much causes pain. Right now, I am sitting at the computer typing and I have an occasional twinge of pain, even at rest. The next step is supposed to be an MRI, but I'd like to have an idea of what we're looking for and how it will be treated before heading down that route (expensive procedure and time-consuming, with a nursing baby that I cannot leave at home to go and have this done). Any thoughts and suggestions are appreciated. I am in the US and have private health insurance.