Hmmm. That sounds tough.
I think I'd do some food eliminating, although your food diary isn't highlighting any patterns, some foods get in everything so go across foods (like you often find soya in a lot of different things you might not expect).
So one by one cut out a food/food group for a month and see what happens. Dairy, wheat, soya etc etc
I'm amazed apple's constipate her as they usually help, the pectin in apple's has a balancing effect of firming up loose stools and softening hard... So I'm puzzled why they should constipate her. 🤔 that said, my niece finds apple's give her a unhappy tummy, but it's the skin specifically if she peels it she doesn't get that... and we think it might be the wax that is put on the skin to extend their shelf life.
Does she still get breast milk? I presume not as you haven't mentioned it, but you'd need to look at your diet too if she was.
Another thing to try to help with symptoms, you could raise her mattress a little so she is slightly higher at the head end. This can help the gas escape more easily then a fully prone position in the night so might help reduce the amount of waking. You can put books or similar under the mattress to raise it a bit.
Another idea, is she very active? Does she do a lot of rolling, and crawling etc? The stronger her core muscles are the better for a windy tummy because the muscles help reduce the bloating effect and move it on its way naturally. Good muscle tone holds the gut in place better, so wind isn't building up through the day as much as with softer muscle tone which allows the gut to expand more. So, I would also encourage anything that gets her using her core muscles, ball pit at soft toy place, crawling around, walking if she is walking, rolling over... Anything like that.