Mind to describe exactly where the pain is located?

From what I gather, the condition arises because running/cycling are pretty much in the same plane of motion. Once I developed a good case of peroneal tendonitis, I could aggravate it from either running or cycling. PT exercises using resistance bands et. al. were somewhat helpful eventually but time consuming. What finally cured it for me quickly and thoroughly was consistently spending a few minutes walking sideways each direction on the treadmill for my post workout cool downs. If you've got a treadmill available afterwards, post workout (run / bike) alternate sides every thirty seconds for 3-4 minutes and see if that doesn't help. Vary your stride length, too, while performing these. Best of luck.

Edit, NM on the above, I've had both peroneal tendonitis and piriformis syndrome. Above advice was for piriformis. But regarding your peroneal, yeah, cycling would bug me with that one, too. My pain was at the upper attach point, and I could reach down and massage my leg sometimes as I was going if it started getting painful. That's a tough one to get over because it's not easy to get at those ligaments. Lots of massage is what finally helped me with that, as I never found a PT that helped. But you can get over it eventually.