After I rested and iced my foot, it felt better. I walked around and the pain was gone or so I thought. As I got out of bed and walked barefoot across the room the next morning, that same pain reappeared. It wasn't as intense as on my run the previous day, but I figured that was because I was walking not pounding the pavement. Once I put on my shoes, it seemed to disappear again. I was baffled. Running—pain. Barefooted walking—pain. A few days passed and trying to ignore it didn't seem to be working, so I called the doctor who had treated my stress fracture.
The doc checked out my foot. He pressed firmly on the area of my foot where the pain originated and "Eee-owww!" He looked up at me and said, "Morton's Neuroma. You have Morton's Neuroma." Sounded bad to me, but he quickly explained that I was having a problem with a nerve in my foot. The doc further explained that a neuroma is a noncancerous growth of nerve tissue. He said it can occur anywhere in the body, but when it occurs between the third and fourth toes causing sharp burning pain or even numbness, it's called Morton's Neuroma. He also said it was pretty common in runners. When you run, as you land on the ball of your foot, the resulting pressure causes the nerve tissue to get squished by the bones of the two toes, resulting in the pain.
My first question to the doc was, "What causes it?" His response, "Don't know." He said it's been studied but no one seems to know exactly what causes it. Sometimes it appears after trauma to the foot, but other times it just seems to appear for no reason.
Second question, "How do we get rid of it?" Doc's response "Several options—wearing a metatarsal pad, corticosteroid injections, or surgery." I was about a month away from running a marathon, so the injections or the surgery really weren't good options. He preferred trying the metatarsal pad first over the other two options anyway. You're not immediately able to run right after having the injection and sometimes you need more than one and surgery doesn't always solve the problem. 
So, we opted for the pad. But I was confused. Seemed to me that if I put a pad under the ball of my foot, it would cause more pressure, resulting in the shooting pain in my toes. Come to find out, the pad doesn't go under the ball of your foot. Instead, the pad is placed just behind the metatarsals. This way when you run and land on the ball of your foot, the pad actually receives most of the pressure. The direct pressure to the metatarsals is decreased alleviating the pain.
He gave me a pad and showed me where to place it on the insole in my right shoe. It had an adhesive backing which secured it in place. I went for a run that afternoon and it worked! No pain. Now each time I buy a new pair of shoes I also buy a new metatarsal pad. Funny how I can hardly walk barefoot, but I can run a marathon! Thanks goodness for metatarsal pads.
