This is a very good analysis. That comes to one very obvious conclusion. It's the defense of course. Fulham are creating chances at a high enough level, but they've given up an appalling amount of goals. However, I do have one big criticism with the article. It completely ignores the time that Felix Magath spent in charge.
In that disastrous run of seven games, Fulham conceded 18 goals. Let me say that again. Fulham conceded 18 goals. That's 2.57 goals a game. In the 27 games that Kit has been in charge, Fulham have conceded 40. That's 1.48 goals a game. If you project that lower total over the season to this point, Fulham would have conceded eight less goals. While giving up 50 goals would still be bad, it moves Fulham from 23rd in goals conceded to 17th. While not great, that is a big difference and wouldn't be completely out of line with the rest of the midtable.
What I'd really love to see is this study repeated with Magath's time thrown out. Would it change things? I don't know, but it just might.