Greg, just some thought's, one of the things that takes the time is the 10x over sampling on the adc input, you could reduce that to 5 or even remove oversampling altogether, and get an immediate speed increase of 2-10x enabling you to then select the slowest cpu clock speed.
The LM385 V ref is fed via a 22k resistor which equates to a permanent load of approx 130ua. It needs a certain amount of power to produce a reliable voltage but the resistor could be increased in value.
100k would give 30ua but may be too low for reliablility, something in between say 47k may be better and combined with the slowest cpu speed may make a big difference to current consumption.
I'm also intending to adjust the low V setting to about 2.5v as the amount of available power is very low once the cell V drops down to these levels.
Although the cpu will function to below 2V, it's pointless pushing it until it locks up and has to be hard reset, some V overhead is a good idea.
To keep it all in perspective, your 400ua drain is probably below the self discharge rate of the 100ah cells anyway
It will run for over 80days for 1ah consumed