Confused, help needed!

Forgive me in advance for the long post…

I’m so happy to have found this forum a few weeks ago and have been a silent reader, gaining so much useful information for my situation. My baby girl is 2 months old today and has been struggling with reflux/allergic colitis since she was 4 weeks old. I have a 2yr old son and as soon as my daughter started blood curtling screaming in the middle of the night, I knew something was not right (not to mention her poop had turned green). Our dr tested her diapers (positive for blood) and diagnosed her with reflux and allergic colitis, prescribed her with zantac, and told me to go off dairy and eggs (my son was allergy tested at 13mo after he broke into hives from his 1st birthday cake – dairy and eggs were his 2 strongest reactions). After 2 weeks without dairy/eggs she was doing so much better but still had episodes of pain/struggling to poo/screaming/etc. We went back to the dr at 6 weeks and she told me to eliminate soy and wheat as well. Things were going pretty good, eating tons of fresh produce, chicken/grass fed beef, and rice. Then she had a HUGE flare up, wouldn’t nurse, lots of screaming, not sleeping (1st time it impacted her sleep). The only different things I had eaten that week were corn tortillas and oranges. After researching on this site and others, I realized it could be the citrus. I debated what to do for a couple days (continue with just no dairy/soy/wheat/eggs/citrus? or follow an elimination type diet because I didn’t want to see another flare up ever again (I know, unrealistic, but was at my breaking point emotionally seeing my baby girl in so much pain). So, I decided to go on my own modified elimination diet (based on what I already had feelings she could/could not tolerate). I picked chicken, rice, pears, potatoes, grass fed beef, green beans, carrots, olive oil/salt/pepper. On the 4th day, she had her 1st full day without having one pain episode, all of her poos were the right color (still mucousy which I realize takes time), and she was smiling/happy (finally!). We had 3 days in a row of this and 2 nights ago my husband asked if I was allowed to have squash. I told him its in Dr Sears elimination diet, so assuming it should be fine. We made a rice pasta with chicken and yellow/green squash with olive oil/salt pepper. We had it for dinner and she had a great night. Yesterday I ate the leftovers for lunch, and then we made the same meal for dinner again (husband was happy to have variety, he’s been doing his best to stay as close to the diet with me for support). She had a great day yesterday, but then last night she woke up sooner than usual, and she was screaming in pain. I immediately felt panicked, its just been a long 5 weeks and I thought we were finally on the right track. She only screamed for 15min and then gave up and went back to sleep without pooping. This am she woke up happy, pooped and went back to sleep. She’s basically been sleeping all day, just waking up to nurse and go back to bed. No more episodes, but I’m super paranoid because we went 3 full days and 2 nights without any apparent pain.

So…finally where I need help 🙂 1st, during the healing process do babies still have some bad screaming/struggling to poop/hard belly/loss of sleep moments even if you’ve figured out the right combination of foods that seem to be working? Or is her episode in the middle of the night last night an indication that she reacted to the green/yellow squash? Her poops look exactly like they did the last couple days (right color, a little less mucous than at her worst). Is being extra sleepy sometimes an indication of healing? Or should I be concerned? She’s honestly been a pretty good sleeper thru all of this, just sometimes needs to be in bed with us, but she seems to be even more sleepy than usual today. I’m just afraid to overreact and cut out the squash, but I’m also afraid to keep it in and have her get worse again. My 2nd question is how long does it typically take for a flare up to normalize again. The week that made me decide to do total elimination made me think it took almost a full 6 days since the last time I had oranges to see ANY improvement…is that normal?