I know how you feel! We've seen a mama fox and her two kits next door in daylight, two days in a row, in my parent's driveway. She's apparently got a den overlooking my parents new house, which is just over the bank from my coop. I'm nervously watching my quarantine pen, which is not as secure as I would like, because it has 5 new pullets in it now and it's at the edge of the field we have our coop in. It's on the list to receive some serious upgrades next year, but right now I'm saving to buy good wire for our permanent run, so I've reinforced it with what I have on hand and I'm checking on them frequently.
It sounds like your coop and run are very secure, good job there! I'm not sure what you can do while they are free-ranging, other than being out with them all the time, or using tractor for the times you want them ranging.