Oh, I did all of that, but I never got to the point of testing it in-game. When I saw all the "conflicts", I just assumed it was FUBAR.
I just did the December store files, since I wasn't sure if I had included those, to make sure that it wasn't a December issue, and the screen closely resembles what I got when doing the whole thing. While I admit I haven't had time to thoroughly check each item, nothing exploded when I went in-game. I would be interested in seeing if the conflicts are indeed superfluous, or if there's a deeper issue.