Begin walking barefoot on grass as much as possible. 10-15-20 minutes day or mor eif you can. After running, start adding barefoot strides or jogging to your cooldowns. 5 minutes jogging one day, some strides, then run normally. If all is well, 8 minutes jogging, the some more jogging and strides the next day, then a third day with jogging/strides, then back to normal. Keep evaluating and increasing by 5 minutes a day until you are comfortable running barefoot 30 min at once.
If you live in a cold area, get a Nike Free or Puma H Street.
Change your street shoe to the H Street now and walk around in that. Do calf raises with the soleus and gastroc (bent knee/straight knee) lowering slowly. All of this should help you transition to start running in flats. 5 minutes, 10 minutes, very gradual until all your running is in flats.