I think our best bet, when everybody's fit, is an Atletico Madrid style 4-5-1/4-4-1-1 from last year.
Herrera - Carrick - Blind - Di Maria
Mata
Falcao
Obviously Rooney always plays, but let's ignore that for a second.
In this formation, Herrera is nominally right-sided, like Koke. Di Maria similarly on the left, like Turan. Carrick-Blind perform the same duties as Gabi-Tiago. Mata, like Mario Suarez, plays as a SS/CAM. And Falcao, of course, like Costa.
Di Maria and Herrera can support the fullbacks, when needed, but are not consigned to the wings. Rather, their position is structured, without being limited, and creative without detriment to the defence. Both are hard working, so that helps. In most games, however, a Carrick-Blind central will provide more than enough defensive cover. Yes, they're a tad slow, but both have excellent positioning and vision to compensate for that.
Mata has complete freedom to roam. He can maybe harry the opposition midfield a little, but his primary role is to feed Falcao, and get into advanced positions himself. For harder games, with strong opposition midfields, maybe put Rooney in there. Or, on current form, Fellaini.
Falcao can do what he does best.
For width, Shaw and Rafael. That shouldn't be a problem - two great attacking fullbacks.