I agree with you in every respect:
1) As soon as the weakest cell hits 3.6V, turn everything off.
2) Rely on an Ah counter as your fuel gauge. Even better if your Ah counter has the ability to derate your controller when things are almost spent.
This seems to be a good one for only $75:
Instrumentation :: JLD404 Programmable Battery Meter - Thunderstruck Motors - Electric Vehicles, Electric Vehicle Accessories and Electric Vehicle Components. We have electric motorcycles, electric bicycle batteries and controllers.
I have very limited electronics knowledge, so coming up with a device for each cell that trips the charger when the first one hits 3.6V will be a challenge, but this is what I will do.
Now another charging question. Let's use the Kelly 72V/10A charger that I used to own as an example. It had a constant max voltage of 88.2V, and on 25 cells that is an average of slightly more than 3.5VPC. I imagine that once 88.2V is reached, most cells will be right around 3.5VPC but a few will be lower (lets say 3.4V) and few will be higher (lets say 3.7V).
Once the charger holds 88.2V for, say, 10 minutes and is pulling back the current more and more until it decides to switch to float (82.8V), what will the voltage do on the higher voltage, weaker cells? Will they stay at 3.7V or will they continue to increase past 4.0-4.5V (because they are full) while the stronger cells catch up, eventually causing a disaster?
My only experience so far is with lead acid batteries, which simply start to bubble and gas when the voltage goes high. No big deal.