Hi just read through your thread.
It sounds to me like something is waking her at night but then she realizes she needs to wee, linked to the recent PT, although not necessarily communicating this straight away.
Is she crying or calling out when she wakes at night?
I think I read one night she went wee in the night and in the morning her nappy was dry but I'm wondering if she is getting dry at night, has it just been one dry night nappy or more than that?
Is she showing any reluctance to put her night nappy on before BT?
Do you have a small potty you can put in her room to make night wees less stimulating than going to the bathroom? With mine I leave the lights off (just little night light type thing) and will only whisper to him if any talk is needed, if he tries to strike up conversation (other than what is vital which would be a wee, pain, bad dream, water, those sort of things) I say it is night time, no chit chat.
WRT naps, I really think a set nap time with set BT works well at this age on 1 nap. Set nap and BT still allow for the need of a slightly earlier time, for instance a very busy, stimulating or physical day might lead to the need for EBT, but it would be say 15 to 30 mins earlier than the set time rather than counting A times which can move nap and BT quite considerably.
A quick glance at your EASYs it looks to me that you get the longest night after a shorter A to BT (and the worst nights after a long A to BT - regardless of total A time across the day), which is how my DS was, he could cope with an early wake and long A to set nap time but could not cope with a long A to BT. Mull it over, it might sound like "that's it!" to you, or it may not.