I realized that by using the power loss signal from the RTC the voltage may be too low at that time to properly tick the clock. I'm going to try a voltage regulator that includes a power-good output. I've ordered a few MCP1755's and will hopefully get to try them out this weekend. Another benefit is that it will be easier to test the power-fail worst case timing as the regulator has an enable pin as well. With that I can use an Arduino to watch the DS3231 1hz signal that I'm using to tick the clock. When it marks a new second I can disable power which will require the "backup" capacitor to supply power for the entire tick and then for the time to save the position information.
A second benefit is that the backup capacitor can be much smaller! I calculated that a 220uf capacitor would just have enough at the current tick timing I'm using. I plan on using 510uf so give me some wiggle room for various timing that may be required adapting to other quartz clock movements.