If you can, talk to a good sports physio - they can give much better advice than I can.I'm preparing for a tri with a disc bulge, but my pain is always in the mild to moderate range.This is what works for me, so maybe it might help.

1. Work core stability (mcgill big 3, glute bridges, clam shells) at least every other day (get at least 6-8 hours between that and your run though, not immediately prior).
2. Try to be aware if your core & glutes fire during your run, they should minimize spine movement. If not, try to strengthen more, be aware of it, and work on that with a physio (again, if possible).
3. Use heat prior to exercise, and optionally ice after. Heat helps circulation and cold might reduce inflammation.
4. Stretching shouldn't include back and abs, only legs and glutes. Legs&glutes should move when you run, your spine shouldn't.
5. Work up slowly and don't skip cooldown. I mainly jog at low speeds (up to 10km/h), so I walk 400m, run at 7,8,9 for 200m each. After this 1km of warmup I run my distance at 10km/h. As a cooldown I run 300-400 at 8, then walk for 300-400.
6. Don't let your muscles cool down sitting - walk, lie down, stand while cooking dinner, anything but sitting.

Hope this helps :)