1. I don't use external diodes and don't really understand for what they would be needed
2. Yes, you can only connect one flatpack in a series, otherwise you will blow the arduino. However you can connect two that are in parallel, for example the two bottom ones.
3. I'm actually using max voltage on both currently, so 57,6 V each.
4. You can't set a permanent max current, you can just control the current of the one connected to the arduino. The other one is following because they are in series. The PID determines current via voltage regulation.
5. There's no such command as far as I know. Power off the flatpacks first before you disconnect them. When theres no current flowing anymore it's safe to disconnect.
6. So far there is no list I guess. You can extract the different commands out of the code and forums.
Some additive notes on the questions:
1. On the endless-Sphere forum there's a guy called DoctorBass and he is a kind of super specialist on builing electronics and especially chargers. He always insist on having a diode parallel on the output. (anode on minus, cathode on plus) I tried to look up the thread but there are just too many post about diodes on outputs. I discussed this also with Remmie and he remebered as it has something todo with the series connection of the FlatPacks and having just one load. In some rare cases there can be a reversed voltage on one of the rectifiers for a short period of time. With this diode you always protect the FP agains any reversed polarity for just €2,50. Use Schottky diode DSA70C150HB, middle pole is cathode and outer ones are Anode's. There are 2 diodes in one package.
http://www.conrad.com/ce/en/product/160616/IXYS-DSA70C150HB-Schottky-DiodeThey won't get warm, as they only work in a very short period of time. Put some heatshrink over it to islolate the housing.
2. And the FP will also blow! At least the CAN interface will die!!!
Remmie and I are currently working on code and hardware to control BOTH flatpacks, for a dual FP setup or a Quad setup. The bottom one communicates via a standard Arduino and the top one communicates via an isolated Arduino. Both Arduino's are talking together via an I2C connection.
If all is going to work as the idea, current is maximum controllable. So you can charge on every power connection available.
No matter if its a single 5A camping circuit or a tripple phase 22kW station.