pain in third metatarsal

I have been having some pain on the top of one of my feet, arising from just behind the third metatarsal. I first had this pain 3 weeks ago. I have been training for a marathon since January.
The pain first arose after about 4 days of rest from running, on the day I started up training again (I had a cold and took a few days off to get better. This issue started on Wednesday April 5th.
I’m in my late 20’s and am healthy, at healthy weight, etc. Once in awhile I have a small cramping feeling in one of my feet, but usually it will go away after walking around or running a little bit. So, I didn’t think much of the small pain radiating from the middle of my foot that day, and decided to run through it. During and after running that day (I ran 5-6 miles), the pain gradually got worse. The next 3 days it was very painful to walk. I iced the injury and kept it up. It got a little better but I still had it checked out by a podiatrist the next week (6 days post-injury). She took x-rays and everything looked fine (no stress fracture indicated). She also said my foot bones look thick and strong, and it probably wasn’t a fracture. So, she made me a temporary orthotic to rest the 3rd metatarsal, which I have been wearing most of the time. She said to take another week off before trying running again. I tried running again 2 days ago (one week after my podiatrist visit) — it was okay for the first 1/10th of a mile, I’d say, but gradually got worse. After about a mile I stopped and had my husband come and pick me up as I didn’t want to risk injuring my foot further.
It seems that the injury really hasn’t gotten much better over 2 weeks. It’s a little swollen and pretty painful if I push directly on the injured spot. It’s not painful pushing on any other metatarsals. A tendon extending from my lower leg to my foot also feels tight. I have been biking, strength training, and doing pilates to keep up my stamina, as I really want to get back into running. If you have any other suggestions as to what this injury might be (besides a stress fracture), or what I should be doing, please let me know. I have tried icing and also soaking it in epsom salt (I just started that yesterday), to see if that will help. Please let me know at this state what would be good to do. I don’t really want to have to go back to the podiatrist, if this is just a muscle strain or something similar!
Thanks so much for your time.