So as someone whose run flooded twice this past winter...

yeah it sucks. I got lucky as far as the coop at least because my coop is slightly elevated, like 6", on concrete blocks and skids, so the water went under the coop and the wood in the body of the coop stayed dry.
How high did the water go in the coop location? Wondering if any of the wood was compromised, in case you wanted to reuse some of it.
Digging trenches and drains won't help much if you're in an area prone to flooding or heavily saturated with ground water, just no place for water to go. Do you have any spots you can use on your lot that sit up a little higher and aren't as prone to flooding? That would be ideal. Also consider building the coop on some sort of foundation, blocks, skids, etc. to further increase the chance that the coop stays dry in case something like this happens again.