Just to follow up, I was ultimately able to straighten this out. When I first called the Premier line to inquire about the disappearance of my E+ aisle seat the agent did offer as a courtesy to move me to another JFK-SFO flight on 10/13 with E+ aisle availability which I declined.

After simmering down a bit, I checked some of the later flights that day as my schedule was flexible and I noticed R availability on the 5pm JFK-SFO #512. I called the Premier line back to see if I could switch to this flight as a no fee change was offered to me earlier this morning. After reviewing my record, the agent saw my previous seat mix-up and immediately moved me to the 5pm flight at no cost and also immediately confirmed my mileage upgrade to seat 1B. On balance, a very good outcome. ^