We're doing better the last day or two. Yesterday I tried going in around 35-40min and staying with her over the 45minute transition, but I was in there for 45 minutes and she would scream for a couple minutes, sort of calm down for maybe a minute, then scream again. I finally couldn't handle it anymore after about 45min and left (she woke up soon after).
Her last nap yesterday and then this morning I just left her and she would cry for a minute or two a couple of times, and then she kept sleeping. Much easier on me and a better result in the end too. I don't know if maybe me being there was more stimulating than helpful?
We've been working on extending the awake times as well, she initally starts getting fussy around 45min to an hour of wake time, I've been taking her to change her diaper at that point, seems to distract her and put her in a good mood for a little bit. Then as it gets closer to nap time I've been holding her and walking around the house or reading to my older one. Doing this we've been going 1hr10min - 1hr 30min in the last couple days, which has seemed to help her naps too.
Happy to be making a little bit of progress!