So Dybala, Manzukic, Chiellini and Marchisio are out

what a mess.
I'll try to be optimistic and hope that Hernanes has a good game. I'd still go for a formation the team is comfortable with. 4-3-1-2 with a full load of work horses.
I trust Hernanes more in a diamond midfield with Pogba, Asa and Pereyra running around him. They are all hard working, skilled with the ball, defensively solid and very fast. If they get their decision making right then we might have a shot in counter attacks. We also get to keep Morata and Zaza in their positions as ST
I don't trust a front 3 of Morata and Cuadrado on the wings. We get nothing offensively out of morata on the side and Cuadrado has terrible decision making and finishing that I expect would ruin our counter attacks. I anticipate a lot of frustration from us fans. A 3 man midfield against Bayern's will also get slaughtered.
4-3-1-2 is the way to go. 4-3-3 maybe after Bayern tires in the second half.