We then have an activity which can last 30 minutes to 1.5 hours.
Remember that A time starts as soon as your LO wakes up, so it includes the time that she's eating. Your child sounds OT (hence the very short naps), and it's possible she's not showing tired signs until it's too late, or showing them too early - my DD would yawn exactly 30 min after waking up, but it was too early for a nap. (My DS would keep going until he was ready to drop and then start shreiking right away - I thought it was normal for a baby to scream to fall asleep, until I started BW and realized he was very OT at that point).
Also, for the very young, you may need to help them stay asleep for an extra 10 min once they fall asleep to get them past the jolts. Granted, once they are screaming hysterically it's hard to calm them down. I also use the patting as a way to help sooth my DD initially, without the rocking, since it helped her stay calm and fall asleep in her crib, before any crying would start. As she's gotten older, I use less and less patting to help her fall asleep and she's just starting to be able to fall asleep for naps without any patting sometimes.
You also want to be careful with when you are feeding your LO. If she wakes significantly before 3 hours you can do an activity first before the feed, so you have more of an AEAS routine. This way you can try to prevent a snacking problem when the naps are too short.
These are just some of my initial thoughts, I'm sure there are others who can guide you further. What does your typical day look like in EAS format?