I'm not sure if I'll be of any help as my ganglion cyst was on the rear outside part of my left foot. Anyway....here's my story as briefly as possible....
I was in my mid 20s at the time (38y/o now) and working 12-15 hour days 7 days/week at the time so having a pain my feet hurt and also a shooting pain up my left leg just wasn't something I was paying attention to. One evening after a long day on my feet one of the techs noticed what was the size and shape of a squishy pingpong ball hanging over the side of the flats I was wearing. (oh have I come a long ways in taking care of my feet with the shoes, orthopedics I wear since!) I just remember a little shreek coming from her and her pointing with one hand and her mouth over the other.
Skipping the details I went to the first doc who charged me $100 to just drain it and then it would of course simply fill back up in no time. I began to grab a needle in the pharmacy and just drain it myself even with my fears of such!
I of course had to eventually resort to outpatient surgery by an orthopedist. He removed it, it was benign, all was good. What I do remember however was the slowness of the healing and how bothersome it was! It was just on the part of my foot where most all shoes...tennis shoes, etc....hit the back of your foot and no matter what I did even after the stitches had been removed it kept coming back open. It's been awhile now of course but I remember calling the nurse alot searching for a way to get the skin to stay in place so it could bond together and heal. She gave me several suggestions such as butterfly bandages, etc but none seemed to work. Finally she suggested taking a regular bandaid and removing the middle pad with some scissors and using each sticky side that was left and with the skin held in place and as much as possible just wearing some houseshoes or something simlar so nothing would rub against and remove the bandaid pieces. I can't tell you just how long it took but I'm guessing 2-3 weeks and I was finally to the point where the skin stayed together and I was on my way!
I need to reread your post but I remember you saying you have the stitches for 3 weeks right? I would say that's definitely a good thing, particularly considering the cut is on the bottom of your foot. It would be almost impossible without complete immobilization for your foot to heal without having stitches in for that length of time. I believe mine were in for 5-7 days. No more than a week I know. That will be key for you!
As for how I'm doing now? I will occassionally feel some nerve twitching in that area of course but certainly nothing to complain of. I'm very active physically and play lots of tennis so that should tell you alot right there concerning your running. You'll get back to it but just give your body time to heal before jumping back into things and making it worse. I have learned too many times the hard way now that it is SO much better to wait, let it heal and then get back to business. I know you're feeling like you're falling apart and will never get back into the shape you were, etc but believe me, allowing your body to heal first will put you miles(literally..
..) ahead! Let the foot heal first THEN slowly build back up but not one second prior to it being healed. You will only be in for setbacks and frustration.
I hope that helped in some sort of way. Not being able to do what you want and are used to doing is frustrating but at least now you have it out of the way and will be glad and better off for that. Just try to be patient in the meantime and talk with the physician about some other type of exercise you can do so you won't feel as if you're completely losing ground and work on upper body.....just try to get outside your box and find some positives from it. You'll be glad you had the surgery done but once again....be patient and let it heal. (Did I emphasize that enough?lol!)
If I can help at all please don't hesitate to ask......Like you I was unable to find anyone with any similar type cyst and the doctor told me as well mine was extremely rare and he and the other surgeons around had seen nothing like it before.
Hope you have a wonderful Christmas and holidays!