I had this same concern when I first purchased my 2900D. The front jack-knife sofa was really uncomfortable to sleep on. After a bit if time, I decided it needed 2 improvements.
1. The 3 sections needed to be aligned so that when in the bed position they made a flat surface. The center table section was almost 1.5 inches higher than the 3rd section that was under my shoulders. I added vinyl washers between the sofa sections and the frame wherever it was low and got it evened up. And why vinyl? They eliminated any squeaks from the sofa where metal rubbed against metal. I found this helped the comfort. I got good feedback from guests who slept on it before and after as well.
2. The foam padding is not the best in 2 places. The 1st section which is the seat for the sofa position seems to be compacted from more use as a sofa. And, the center section which folds down to be a small table has less padding. In general it's not high quality foam. I'm considering recovering the sofa and changing the foam at the same time. If I made all of it at least an inch thicker it would be far more comfortable. I know it would fit if I removed the 4th section,, which is a fabric covered board attached to the wall. With it gone,,,, there's a 3 inch gap to fill... I'm wondering if I could just move the sofa 3" closer to the wall or make the 3rd section taller and have it pivot up and fill the gap. As you can probably tell,,, I haven't done this yet (for several reasons) but it's on my list if to-dos
Sorry, I don't have the perfect solution. If you can find a reupholstery shop they could advise and do part 2. While they have it apart they may be able to see why sections don't align and fix the frame shape,,, or add the vinyl washers like I did to make flat in part 1.
I'll see if I can find a photo I took after getting it leveled up and attach it here.
Larry