Well I cautiously went ahead and wired up the charger again (shown here attached by ring connectors), without its 'safety-net' light bulb, and it was fine. Then I powered down and attached the battery bank in the way you described, attaching the positive corcodile clip to charger positive terminal, and the negative clip to "pack negative", and using a jumper lead (the yellow one here) with clips to crosswire the pack negative with the top of the resistor closest to the control circuit (the far left one as seen from the top of the board).
When I powered it all up, the main LED came on green but it didn't do anything, even when I twiddled the adjuster, and no yellow LEDs came on at all. But when I attached the header to the EOC disable, the main LED turned orange and the charger came to life
The FETs become only slightly warm, and everything else was stone cold, not surprising as the charger is the weedy 2.5A one I use for my SLAs. The pack charged until it equalised with the charger, which switched itself off after a while. The voltage of the pack got raised from 80.2V to about 84V.
Presumably no orange LEDs came on because of the low voltage of my charger (84V) with respect to the ideal maximum pack voltage of 87.6 (or 86.4 at 3.6V per cell). And presumably also the charger stayed green without the EOC disable because no cell circuits were attached (is this right?)
This brings me to a point I quite urgently need to address now. I asked for the charger I ordered to be set to 87.6V, but presumably this should be more like 86.4V if it's working at 3.6V per cell max, right? But why does the charger voltage need adjusting at all as part of the callibration you describe? Isn't 86.4V more or less exactly what it should be?