Some photos might help, but the subframe connectors will not be parallel as the rear subframes are narrower than the fronts. That means you can't line up the connectors in a straight line with the front subframes, they need to be slightly angled to meet the rears. Also, the seat mounting points are not equal on each side, the drivers seat mounts are about 3/4" further inboard for some reason. I'm not sure if the connectors have the seat reinforcement brackets already attached or if they are separate, but you should make sure those are in place and aligned before welding to the subframes and finding they won't line up either. If you have those on the wrong sides, it might also explain you misalignment.