My DS also had a 40 min sleep cycle. His A time needed to be long enough to see him through 3 cycles to get a 2hr nap. It means learning to transition twice in the nap (rather than once for a 45 min cycle and a 1.5hr nap), maybe part of it is increasing the A a bit and maybe part is teaching the habit of the longer nap. Can she do another 15 min on her A time do you think? Then perhaps try W2S on the second transition (go in before that usual wake up time of 1hr 20, say 1hr 10 and either begin shush/pat or have your hand hovering over her to sooth her over the moment she starts to stir) to teach her to nap longer.
If you can get even 1 2hr nap it would help get through the day more easily. Plus if the morning nap is 2 hrs she can likely to a little longer on the second A time too which would be another help.
Is she not coping well with that long last A time then? Some LOs don't mind it so if she's okay with it and your routine is consistently like this and works then I'd leave it. If she's a terrible fuss and getting OT I'd increase the earlier A times even if it didn't result in a longer nap, just evens out the day more.