Hi Pro
I'm not going into Technical mode, but will stay in english
The reason for the dry plates is an easy one its called lack of maintainance,
and I can see why it doesn't get maintained, being stuck under a seat.
this is the reason why it wouldn't start after nine days standing. You might get away with just a recharge but its looking like a new battery on you list, when the winter finally arrives you will see what I mean.
By the plugs I asume you mean the screw caps?? If so then yes leave them off while it charges, this helps the gas's escape better they will still be present over and hour after the charge has finished., bit of advice though, make sure you switch the charger off at the mains before disconnecting the battery clips.
yes you are right in the Black then Red but this only applies in that sequence if your battery is still connected in your van.