That's a problem I've been having as well. I've noticed that you need to cut away a bit of the bottom of the inner door, where the mould injectors were, cut a bit more than just removing the injectors, the two pieces that form the inner and outer parts should be even with each other, forming one flat surface. That helps a lot. also, finishing the upper structure of the pod also helps line up the pod doors, don't ask me why though...