Hi there, wow there's a lot going on, hugs. My reflux bubs had to be taught to sleep, for the first 3 mths we bounced him on an exercise ball while holding him upright. Then he also napped in his swing until he was too big for it - while we did sleep training around 16 weeks of age. So I understand :-)
First I want to ask if she's on medication for her reflux and how you know for sure it's not bothering her? The thickening does help, we moved to that at around 5 mths and saw a vast improvement BUT he still needed meds to control the acid.
What you describe in your second paragraph really does sound like reflux to me.
Could you also post your routine, we can take a look. Even just past 2 or 3 days will help us.