The problem I had and is probably the same you are experiencing when my right rear handle carrier had the same issue (not lining up and handle not sitting flush to the door) was that when I installed the new carrier, I did not get the carrier
UNDER the lip inside on the door skin at the top of the carrier. Make sure to lean it in so the top of the carrier goes under that metal lip in the door itself. If you look inside real close, you can see it. I struggled with this for an hour before I figured out my blunder.
