First of all, I'm so sorry this baby is going through this & the parents too. It is so hard when our babies are sick isn't it?
Secondly, the doctor works for YOU. Be persistent, FIRM and let them know daycare or no daycare, 3 months of this is too long. We have our grandson with us right now, along with Mama that is having some surgery. He is almost 9 months old and has had runny, stopped up nose for about a week, however, no cough. He too has trouble drinking from the bottle. I do not use a humidifier but a vaporizer. I don't know if that's what you meant, but we use the Vick's Vaporizer that puts steam into the room, not cool mist. We pour in the Vick's Vaporsteam liquid stuff you also buy at the store (it's not in the box) and the whole room smells like Vick's Vaporub, we love it. You have to put in about a pinch or two of salt sometimes to get it going, but the instructions are in the box.
Also, Vick's now makes a Baby Rub for babies 3 months and older. It says to rub on chest, back and neck and that seems to have helped him too. Also sitting in a steamy bathroom before bedtime might help. We use to do this when the kids got a croupy cough (we have 5 kids). We would just sit on the toilet (lid down of course) or if we had room a bean bag chair or other chair, close the door and let the shower run on hot filling the room with steam until the hot water ran out. It's not much fun for Mom and Dad but it sure helped them.
You're doing good with the saline & nose bulb. They hate it but it's a good way to keep her nose cleared out.
You might also see if she might be having a food allergy. Have you introduced something new lately that you could pull back on a while & see if that makes a difference?
And if you can't get your doctor to listen to you, change doctors. I've had to do that too.
Best of luck to you. I know you're all exhausted.