I've had this exact problem. Metatarsalgia is technically the symptom (the pain in that area) - the diagnosis of your actual injury is probably something different. For me I had capsulitis... and it really sucked. It is all gone now, but it took me about 6 months to recover. My advice: When you think it feels better, DON'T go back to running on it again right away. I did this numerous times during the 6 months and each time it came back just as bad. A few things that I did for it:
- took 1 cortisone shot. Quick fix that had me running well for a week, and then the pain returned.
- Advil a few times a day consistently for 7-10 days. Also tried a prescription drug that my doctor thought would work well for 10 days consistently, but for me I didn't respond to either (he seemed pretty surprised that this didn't fix my problem straight-out in 10 days so maybe others would respond better)
- ICE MASSAGE. Not positive that this was what actually fixed it, but I added this as often as I could shortly before it healed for good. Take a styrofoam cup and freeze some water in it, take it out of the freezer and tear down the edges so that solid ice is exposed. Then just rub it on the sore spot for like 8 or so minutes, a few times a day if possible. Consistency is key, just like with the pain meds.
- Switched shoes and got orthotics also. Orthotics were a drastic change so I only wear them in my running shoes, although I got a metatarsal pad for all the pairs of shoes I own. A metatarsal pad (look it up) works wonders for relieving the pressure of that bend in the second toe.
Again, I'd say even when it feels 100% walking, make sure you can press your fingers all around that area with ZERO pain before trying to get back into running. And if you do start running again, stop at the first sign of any pain at all. There's no "running through" this injury.
Good luck and I hope you can get through it a lot faster than I did!