She might be self-medicating a mood disorder. In other words, it is not that marijuana causes her to be irritable when she is off it, but that she has a mood disorder which marijuana masks for the duration of its immediate effect.

The situation with her waking up at night is simple: try sleeping in the living room on the couch, and let her wake up in the bedroom on her own. That would be your experiment. If she sees that she still wakes up even when she is alone in the bedroom, that experiment's result will show her that she was wrong to blame you.

If you have sex before you go to sleep, you can have sex and then go to sleep in the living room.

If you have sex in the morning, vice versa.

If you have sex both before you go to sleep and in the morning, combine the two. Either way, it is a solvable problem provided you have a couch.