I think you are focusing in a very productive area. Another thing to think about is knee angle. Going over the top, there's not much hip angle change, but the knee angle changes. So kick forward with the quad. Once the downstroke starts, the quad phases out and the hamstring comes in. Coming across the bottom, the hamstring dominates as there's not much change in knee angle and there is hip angle change. Hamstring domination continues until the hip flexors take over to lift the foot up to the top. On the backstroke, the ham is all you got to lift that foot. Hip flexors lift the thigh, but until the lower leg starts to dangle, you have to lift the foot with the ham. If think if you drop the ham too early, you're losing power. I keep the ham engaged until about 8 o'clock.

On long rides when I'm getting tired, I'll frequently switch back and forth from being quad dominated to ham dominated to give the other side a rest.

The roughness you speak of is the reason I do a lot of high cadence work. Neuromuscular conditioning, so that everyone knows what to do all the time. Drives me nuts when I see people on here who watch TV while on the trainer. That's when you really need to pay attention.

I used to have a problem with lifting the rear wheel, but got better by focusing on body positioning and bike balance. Which may have also changed what fired when. I'll have to think about that the next time I'm sprinting.

But lets not forget the glutes. They're a powerful hip extensor. I think straightening the back also helps glute engagement. Think about how straight your back is when deadlifting.