(Sorry; hit send instead of quote )
I'm not sure why you're asking questions that only you can answer, but I'll take a stab:
"If I could focus on the family after D Day and live without the AP and her ego boosts without medication, then the A was not due to issues of depression"
Not a question but I guess you're asking did your depression cause you to have the A? Depression is an illness and needs to be treated, so perhaps you treated it by having the A; self-medicating is never a good idea...But you only had to wait one month for proper medication, so I can see you white-knuckling through it. However, the A was your choice; it was not forced on you by your mind & body.
"How could the PA become more frequent and compliant when I was trying to end it?"
Have to answer with a question-what do you mean 'trying'? Unless you were tied to a bed and forced to have sex, you could have ended it at any time. I suspect you were doing a form of hysterical bonding with your AP.
"Why did I not care that my BS was being stalked and why would I continue to let the AP possibly put my BS and DDs safety into jeopardy?"
Because you didn't fear her. It was all about you still at this point.
"Why wasn't the A ended sooner knowing that the AP probably wouldn't be searching out a reason?"
See the previous answer.