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.