As I mentioned before in another post, the kit I received needed a 3mm shim in the neck pocket as well. I ordered a Wilkinson bridge for my kit and when I assembled it before paint the saddles were sitting on the bridge plate and the strings were still to high. For the neck to sit relatively square in the neck pocket the whole bridge assembly needed to be moved over to the controls route about 3 mm. That was using the 2 E strings as guides.
Like everyone else's, the pickup route needed some work as well. I thought it was just my kit until I saw a post here last week or so back.