1. Oscar, I may have a solution for you  I have found the charger works if I first plug the old (original) plug into the charge plug socket for a second, this gives the charger a signal to start charging, then swap over the plug to the battery paralleler one. The charge indicator on the dash display then shows the charging indicator. Both batteries then charge. It is a bit of a faff to keep swapping plugs so I have built a simple y lead with a double pole change over switch to swap supplies. I have also updated the plugs and sockets to XT 60 connectors as the original bike one was showing signs of overheating.

Hope this helps. 

The white plug connects to the original charging socket, instead of the grey one.  I never had any real issues getting the two batteries to charge this way, however, some times charging doesn't start automatically.

I these cases, I find that turning the bike on for a while starts the charging cycle.  I have also found that the charging symbol on the dash doesn't always start to flash immediately, it seems to have to cycle between batteries before the flashing starts.

As far as I can work out, its no longer possible to charge with the charge connector still connected to the original grey plug, I assume this is because there isn't any direct connection to the batteries this way, which might explain why regeneration doesn't work through the paralleler.

The other thing to note is that charging still works even when the isolator is turned off, so it would appear charging is handled exclusively by the paralleler.