I haven't read this entire thread yet (at work), but just wanted to comment that I have 2 herniated discs. One happened in 2009 and one this year.
Cycling irritates the hell out of them. There is something about being bent over in a cycling position and the torque being transferred across the pelvis that lights my back on fire. I once trained 100% on the bike and spin bike. My coach was Kevin Mansker's coach Kirk Whiteman, who trained via functional strength. He calls it "Squatting on the Bike". The program was amazing. Hit the highest power numbers ever...and I had debilitating back pain. It wasn't the program's fault. It was my back.
I would literally be in so much pain I'd have to call out of work.
I had to supplement the program with squats in the gym. Doing low weights with moderate rep counts fixed me right up. To put that into perspective, when I was capable of squatting close to 400lbs for 5, I would just lift 3x10x135lbs. That was enough to create the core strength I needed to not experience pain. I would also deadlift. The pain went away.
(on a side note: When I was looking to push gains in the gym, I switched from squat to single leg press. I didn't try to squat for max weight.)
So, as odd as it sounds, whenever I start having back pain, either from my herniated discs or poor core strength from my "dad bod", the thing that works for me are squats and deadlifts with a moderate amount of weight.