First: You must thoroughly clean coops inside and out, including feeders/waterers, nest boxes and roosts, vents. Soap detergent mixed with a little bleach will work, rinse well.
Second: Disinfect everything I mentioned above with Oxine or Vircon including spraying chicken wire around the pen.
Third: Sanitizing the soil. Since you dont know what respiratory disease you were dealing with, you'll have to sanitize the soil in the pen. If they free ranged, it's best to wait and repopulate the following year.
To sanitize the soil in the pen, there are two ways to do this:
1. You can use steam to disinfect the soil.
2. Cover the whole pen with black plastic, two layers if the plastic is thin "MIL." Make sure
it stays in place. If it's winter time, leave the plastic in place for 8 weeks, during the
summer 4-6 weeks.
The plastic holds the suns heat onto the soil, sterilizing the soil. The sun is more direct
in summer, therefore the shorter time to sterilize the soil.