I don't know if this has been addressed here or not but the LES alignment as shown in the instructions is wrong. There should be a leg of the tower in line with the window. The instructions have you align the gap or space between legs with the window which is totally inaccurate. To see what I'm talking about, check out the kit box side pannel that shows a picture of the completed model. Notice the tower leg is not aligned with the window, now check any of your references that show the the same view of the real thing.
Here is a link to the problem & the fix:
http://www.dehaven2.homeip.net/wiki/index.php?title=Rotational_Alignment_%28of_Atomic_City_Mercury_kit%29
Hope this helps