1. He was puzzled because his mother didn’t come to his room as usual every morning. Although I think it would be better to say, "He was puzzled because his mother didn't come to his room every morning as usual."

I like Andreas first suggestion. It’s a little trickier to keep usually in there. Maybe “...didn’t come to his room as she usually did in the morning. “

I would say that #1 comes closest to the correct version. However, I would make the following correction (other instructors may suggest other correct alternatives): 1. He was puzzled because his mother didn’t come to his room as she did every morning. Comments: I deleted "usually," because it does not mean always, but "every" does. For a different meaning; if she did not come EVERY morning but came MOST mornings, I would keep "usually" but delete "every." Still, delete "in" in either case.

first one