Hi there, welcome to BW forums
Sounds like your LO might be a bit UT (under tired) for her sleeps. The crying and not settling and then being happy when you leave the room could be her trying to tell you she is not yet ready to sleep.
Looking at your routine, it seems her A (activity) times are on the low end, here's a helpful link with the guidance A times by age:
Average A times- BOOKMARK ME! I would increase that first A time from 1.5hrs to 2hrs - if she has been resistant to that first nap you could move directly to a 2hr A time, if she has been going down for it relatively easily compared to the rest of the day then you could first move to 1hr 45 and stay there for a couple of days and see how she settles into the new time. If her nap extends to a more consistent 1.5hrs then leave that A time at 1hr 45, if it doesn't then increase again up to the 2hrs.
The second A time and nap it is not totally clear from your post if the 11am nap is more of a set time nap or if you shift it based on her A time. With a shorter first nap this second A time is around 2.5hrs (might be too long, a 30 min nap could be OT, over tired) or if the first nap is longer then putting her down at 11am makes that A time more like 2hrs which might be resulting in the better 1.5hr nap. You will likely know much more information about this so you and your DW can judge if this nap needs to shift a bit, aiming again for 1hr 45 to 2hr A time. Time the A from when LO wakes from nap 1 and adjust accordingly.
Continue with those times in the EAS routine through the day checking that the last A time before BT is not too long, no more than 2hrs unless you are sure from previous experience that she does better on a longer A time.
If you can record the EAS times as they happen that would be really helpful for us to see and to support you, plus any small comments about LOs mood at those times such as resistant or crying a nap/BT, waking crying and such.
WRT to working towards self settling in the crib. When you do your WD (wind down) I suggest you begin as usual, but then shift her to a laying in arms position rather than upright to your shoulder. This can help LO to adapt to the different position of being horizontal and still obtaining the comfort of being held before you try to put down, also reduce the amount of rocking until you are almost motionless - this is something you can do over the coming days. When you put down keep your hands on her, almost holding her, and use a firm hand to give her some slight movement. Very little movement of the hands around baby or on the hip/back/tummy creates a small rocking motion in the crib and this can be a helpful intermediate step between holding and self settling on a motionless mattress. You can also tell LO what you are doing "I'm going to put you in your cot now so you can sleep properly, I'm still here, everything is okay". You might find it possible to use this method which is weaned in the same way as shush/pat, by reducing and reducing, if LO fusses you can use firmer hands and rock a little more, as she calms you reduce and reduce until you are rocking on-off and with a less firm hand...aiming over a number of days for her to be drowsy and nodding off with your hands off her (leave your hand a cm above her if needed in the early days).
If you prefer to try PUPD again as she gets more and more tired and is calming faster and faster in arms because she is so tired, you can try a very small PU, where you put your hands around her in the cot as though to pick up but then only pick up a couple of cm, she might just nod off like that and there is then less movement to get her back onto the mattress. Again you can leave firm hands on her when you put down so she feels your comfort whilst she nods off on the mattress.
WRT sleeping on her front, you and your DW are aware of the safety guidance already, it is really your choice how you proceed whether to lay on her front or back. The routine times and gentle sleep training with rocking/shush/pat and/or PUPD are the same either way.
I hope something here is useful for you. Do let us know if you need any clarification or if you have more questions...and how you get on.