Hi!! I have severe flat feet also. I completed the program a few years ago and got hooked on running. I was NOT a runner prior to this because my feet would swell up so much! For me, incrementally adding to the running time helped build muscles in my feet. I won't lie, it was painful. But with time, I was able to run 15 miles! I would suggest using K-tape on your feet when you run. Also arnica really helps with the inflammation.
Best of luck!!