Cajos,
Was there a problem before ? Was there some accident or something to the car ?
When my birdcage was apart I don't really remember that there was much movement in the door sills, when torquing the cage down.
I shimmed my cage with a laser level and measured up the frame differences to the factory dimensions and shimmed accordingly. I found out there is not much variation in between the cages, but there is much more variation in the frames.
Anyway my cage fit perfectly with only a minimum amount of shims.
To go back to your door, I trial fitted my body with the doors as close as I could get them when reassembling my body and even then it was very difficult to align them properly, thus the grinding on the bolt holes in the pilar. It solved all my whoes. Then I had to use a little body filler to get the door flush with both fender and quarter.
Hard to discuss this from a distance but if you sill panel broke, i'm thinking you are putting way to much stress on it. These sill panel are glued on the sill, so if it breaks you are trying to bend the cage in a way it was not assembled imo.