So I had to replace a door lock actuator on the right rear of my 97 accord, simple enough. After putting it all back together I cannot get the door lock to line up correctly. Ive tried everything and it doesnt go back the way it was. I tried taking off the outside door handle to get a good look and see if anything is blocking it and I cant figure it out. Ive got a few hours at this point fiddling around with it. When I get the holes to line up its in the wrong spot, Im defeated at this point and the door wont close the whole way

 

It may have to do with window channel interfering with the alignment.

There is this video:

 

This will probably never help anyone but I figured it out. Somehow that area got dented in! If you look in the pic you can see the area that got pushed in that goes from the bottom hole down through the VIN number. I have no idea how or when it happened, but a pry bar and mallet from the inside solved the problem!!