I have trouble thinking that its developmental 40min wakings when she's taking a 2hr nap in the AM, it suggests to me that its an A time thing. That she is lying quietly for a while after she wakes suggests you're close, so I think push a little more and you should hit gold again.
On the bright side, she did get a good nap in there and she's had a good overall amount of day sleep - almost the average amount for her age, just with one longer nap and two shorter ones, yk? That just might be her normal body rhythm and you may find that's what works for her for a while.