I can relate, man. When my girl was born, she didn't sleep through the night for 10 months. Of course, as parents, we try to wean them from that 2 am feeding, but at 2am my willpower is subpar to say the least.
But, on the bright side, it'll get easier soon. You'll all get to feeling better and you'll all start getting the sleep you need.
As far as muscle mass goes, if you've been eating, I doubt you have lost as much as you think. You just don't feel all pumped up becasue you don't get your daily fix. 1 solid week in the gym and you feel good again.
Suggestion: If possible, take a day off from work and sleep. An extra 4 or 5 hours would do wonders.
Suggestion #2: You and your wife take turns getting the full night of sleep. It sucks when you are sick, but you can get through it.
Best of luck.