I got my SE60AHA cells installed in the back of the car. I decided to put all of them in the back and the 25pcs set of SE40AHA cells in the front. They will be connected in parallel. I have a service on-off switch in the rear pack, so I can turn it off and measure both sides individually to see if they start developing issues. I also need to move my main contactor and measurement shunt to the front as well.
In general the parallel bottom balancing seems to be a success. I ended up turning it off already the next morning, as the meter was switching the relay on and off with the cells bouncing above and below 2.7 volts based on load. I lowered the target voltage 2.6 volts for a little while and they just left them as they were.
All cells were at about 2.636 volts after taking it all apart and the 60 Ah cells bounced up to 2.656 or so, if I recall correctly. 40 Ah cells to less than 2.65 V. A single slightly suspicious cell stayed below 2.64 volts. Not a huge difference, but we'll so it does in the long run. It will also be interesting to see how the different capacity packs react to charge and discharge cycles, but I think it'll be just fine. If it doesn't work out I can always take them out completely and/or get another set of sixties later.