Hi there, I can empathise with you here, we've battled with this so long... Try not to despair, it will get better eventually! Just wondering, how is she when she wakes from her first nap? Is she crying? Or just alert and happy? Our DS got into this sort of cycle many times, also struggling with transitioning between sleep cycles. But I think he was also just not tired enough to carry on sleeping - is it possible that your LO could manage a little more A time before her first nap? 40/45mins can be UT as well as OT. It was hard to tell sometimes with our DS because he'd be really alert and would have been happy, only he got so frustrated as I tried to resettle him because he just wanted to be awake - so then he'd start crying. I think what might possibly be happening with your LO is that she her first nap is UT, but then because it was only short, she can't handle so much A time before the next nap - and then she gets more and more OT as the day goes on - as you know only too well.
So in answer to your first question - yes, the A time does include all the time from when she wakes until when she next goes to sleep. Some people find that they can count time in the cot (ie trying to resettle) as worth only half of the time spent out of the cot - if she's quite relaxed and drowsy. But either way, you'll need to get her back down sooner rather than later for the next nap. This may mean bringing the feed forward, although not necessarily. I often gave DS a little tummy time after a short nap since I didn't want to do that immediately after a feed - but only a few minutes. You may then find that the next nap is longer, or she manages to resettle - in which case you don't have to feed as soon as she wakes, but she could have some activity time before the feed if it seems too early to feed and she's not hungry enough.
As for your 2nd question - we struggled with this so much! Our DS never liked the paci so we gave up with that early on. We found that our shh-pat turned into just a hand placed gently on his chest with no sound - maybe experiment with different variations of this and you may find something that doesn't make her so OS but just comforts her enough to get back to sleep. Also don't be afraid to wait a while before going in to her - in time, she may learn to resettle herself without your help. I think our DS often prefers us not to go in, as it just wakes him up more. But of course if she's really crying then she probably needs your help.
The other thing that helped us was using our 'prop' for one nap each day. DS usually slept well (or at least better!) in the sling, so I'd use this to help get him back on track after the first short nap. Then we could usually be sure of one good nap each day, which helped to break the OT cycle that's so easy to get into. We did this until he was about 5mo, and occasionally even after that. Do you have anything like this that you could use from time to time?
Lots of love and hugs - hope you see some improvement, I know how frustrating this can be!