I was diagnosed with Piriformis Syndrome some years ago. I stretch before and after I run, as well as doing hip flexor exercises. My question to those that have it is how do you deal? Leg day was yesterday, and my left cheek/leg is screaming at me right now. As much as I love to run and do squats, I know this is not good, but I refuse to stop doing what I love. Running is therapy to me.
If Damian Howell sees this he hopefully will chime in - but I seem to recall him saying quite a while ago that sometimees Piriformis pain can come from too much stretching. So sometimes stretching helps and sometimes it doesn't.
When you say you stretch - are you doing a Piriformis stretch? For me stretching the Piriformis helped. Another thing that helped was tennis ball massage. It hurts like the dickens - but it really helped.
Lastly - although you need to exercise your hips - hip flexors are not what you need to exercise to help with Piriformis. It's the glutes that need exercising. At least that's my understanding.
"Kick off your high heel sneakers, it's party time."
-- From the song FM by Steely Dan