Wow, if your lower back is hurting much, please take it easy. I overdid something, including riding , recently and hurt my lower back and now it won't seem to go back to normal.
Perhaps you are either rolling your pelvis too far forward, or not enough. You need some bend in the lower spine (lumbar) to absorb the motion, but too much will hurt you. NO bend in the spine is also bad because the spine's only way to absorb motion is through that bend increasing and decreasing. If you try to stack the back totally vertical and stiffly hold it there, the motion cannot be absorbed, only a small amount via the disks between each vertabrae and this is not good for the back over long periods of time. We NEED that spring action ofthe curved back.
Also, having strong core muscles is essential to being able to sit the trot. I don't have them and I dont' stit the trot very well, at least not for long periods of time.
When you have the chance, post a video.