Hi Nina. My name is Eileen. I'll be on SCD 12 years in January. I will try to answer the best I can, but I always refer to the Wellbee's experts 
I personally like to cook my bone broth in the crockpot for 48 hours. I can't imagine 3 instead of 4 would do much harm, but next batch do the 4 to be exact, I followed exactly as told.
I never pureed carrots but I did cook them for 4 hours as we are told to.
I would think that counts towards her 5 days, which is the max.
No yogurt on intro, I'm not sure when I started that. but go slow and do 1 thing at a time, and keep a journal of all reactions as everyone has some foods they can't handle (reactions can be Bowel, headaches, moods, headaches etc etc
I don't drink juice, and would say to stay away from fruit and sugary juice right now, but that may not be SCD rules, that's just me and what I've learned gut wise.
I used to have Ibuprofen compounded at my local compounding pharmacy. I haven't touched it in forever. There are many natural alternatives.
This last tip is in no way meant to take place of SCD, but along with SCD may I recommend (if you have an open doctor) to do a Good Stool Analysis. Great Plains is the one I did. I discovered a lot health wise for myself and son, by looking at the gut, which is the core to health.
Good Luck and God Bless. I pray your daughter gets relief soon. Feel free to ask away,(autumn71a@optonline.net) it's a learning curve for sure. I remember it taking a while to get every anti SCD ingredient out of my diet even though I thought I was being compliant, so don't trust anything, from scratch is best - and Wellbees is so helpful 