Your UK born daughter will need to be registered using
Form MN1 before you apply for her British passport.
SushdMehta's post is quite detailed about the status of your wife after you get ILR on the basis of Long Residence. Essentially, as I understand it, she must go on FLR(M) when you get ILR(LR), unless she will qualify on ILR(LR) herself before 2018, in which case, she must never travel outside the UK before she gets ILR(LR).
If she were to travel abroad on her PBS dependent visa while you are on ILR(LR), her visa would be curtailed when she returned and she would be forced onto FLR(M) at that point in time.
I am not a lawyer or immigration advisor. My statements/comments do not constitute legal advice. E&OE. Please do not PM me for advice.