Would the clear covers stand up to strong winds?

It depends on a number of factors, most notably just how strong the wind is. In general terms we would expect the run cover to remain in place during strong gusts of wind, however, if you anticipate installing the run in an area that is exposed to high winds we strongly recommend that you pay close attention to securing the coop and runs with suitable anchoring points. You may want to look at additional heavy duty ground pegs or marquee ground screws.