Bob Simpson designed the EVD5 hardware to sit in the top of a box of A123 cells. You can see this design in action in the background of the photo above, the blocks of cells drop into boxes and the BMS circuit plugs into the green PCB down the side. Each layer of cells is connected together with a thin plate, and a tab on each of these plates sticks out and is simply soldered to the side PCB. The temperature sensors are also connected via the side PCB. The foreground shows what happens when this elegant layout doesn't quite fit -- you end up with a lot of wires. Bob has more electric trail bike construction photos and riding videos on his website.
To reduce the many wires and many fuses problem in my Thunder Sky battery, I am planning on (almost) only one wire to each cell. The BMS is set up for a kelvin connection which makes measuring the voltage easy. Without a kevlin connection, when I turn on the bypass current, the measured voltage will drop (because current is now flowing through relatively thin wires). This can be corrected in software as the voltage drop is purely resistive and won't change very quickly, if at all. We can see in the graph below that without a correction, the measured cell voltage drops 60mV when we bypass 500mA. With correction, this error is only 20mV. I used gnuplot to fit the line to the uncorrected data, and it appears to have given more weight to the low current end (where there are more points) as we have a larger error at higher currents. (I still need to investigate why I'm getting such quantised data)

Unfortunately, with one wire for each cell, adjacent cells share a wire and current bypassed in one cell will effect it's neighbours. Since the slaves do not talk to each other, the master will have to take care of this effect. Internally each cell's slave only uses the voltage reading to implement an antonymous "dumb" balancing. The master will coordinate normal BMS operation, so this won't be a great problem.