To answer your first question, I would count "nap time" from the time she's in her crib and quiet. And yes, A time starts when they wake and includes changing, etc. When dd wakes from naps she's generally happy and up, but first thing in the a.m. she makes noise, quiets, makes noise, quiets, then plays in her crib for a while before getting up. So if she spends a 1/2 in her crib doing that, I could half of that time as A time, if that makes sense.
Your A times seem about right. I still would keep the same A time or just very gradually try to extend--don't be tempted to put her down super early thinking that will make things easier, imo it's harder to put down an undertired baby than an overtired one.
I still think it might be an independent sleep issue. There's a "jolt" that happens at about 20 minutes and if she's not used to sleeping independently in her crib then she'll wake. It sounds like she sleeps well at night, but day sleep and night sleep are controlled by different parts of the brain. If she consistently wakes at the 20 minute point, you can try staying with her and gently patting or holding down her limbs (whatever works for you) to ease her past the jolts before she fully wakes. Eventually she'll be able to get through the jolts on her own.
When we were trying to extend naps the key was getting in there before she woke fully, otherwise she would never go back down.
How long have you been doing pat/shh, do you do it for night and naps, and how long does it usually take?