Even if you overcome your alignment issues (and they are issues), you are going to rip your SMD headers off the board the first time you try to unmate with so many ofpins at the same time with them being distributedseparated by such vast distances across the board unless you have. Without a separation jig that can pullseparate the boards directly in line with each other. Otherwise, the first time you try to unmate them it's going to tilt, jam, and then tear off some SMD headers.
My experience was with boards that had a single 2x20 0.100", standard force, through-hole header. The force on all those pins adds up as doesand the jamming effect as they getgets worse the farther apart the pins are. If they were SMD square post headers, they would have torn off, and you have more pins and they are spaced farther apart. Going back, I would have used different connectors and I suggest you do the same.