Certain players can't play in my opinion. I don't see Hernandez or Nani is viable options, given their lack of match sharpness, and particularly Hernandez's poor dribbling/hold up ability among other flaws. Januzaj shouldn't be thrown into the lions den at such a young age, and to expect him to be part of a defensive effort against Robben/Ribery would be bordering on cruel. Fletcher can't be reasonably expect to start in such a big game with only 3 days rest, though he's a maybe. If he's 100%, I'd rather he started over Fellaini.
Personally I wouldn't be overly fond of Jones in midfield, given Bayern's pressing and his lack of games there in recent months, but if Rooney's out he might have to play there. Fellaini might be average, but at least he's been playing CM on a regular basis this season, and hopefully he can't be any more crap than he was in the home leg. Moyes is playing him anyway so might as well have him in my lineup.
Without Rooney:
DDG
Smalling Ferdinand Vidic Buttner
Carrick-Jones
Fellaini
Valencia-----------Kagawa
Welbeck