I would adjust her slowly. When you first see what you think is her tired cue, try moving her to a low key activity for 15 more minutes then start her wind down. Try that for 2-3 days and then extend some more if she's still taking UT naps. If her nap is only 40 minutes, then her next A time will be a bit shorter. Again, follow her cues and repeat what you did for the first nap. Once that first nap extends, her next A time will probably shoot up to around 3 hours.
Time in the dark in the crib isn't as stimulating as normal awake time. So, even if she's staying awake it probably doesn't count as full A time.
Let me know how it goes!