Elite cells are the best you can get.
I have a feeling the charger will keep working, but your in a wierd spot for the connectors.
The G&G Chargers and batteries use a mini Tamiya size. I think the actual plug in the back of the stock is a large tamiya, with an adapter on it to let you use the smaller size.
your best bet? Buy the Elite 4000 or 5000 pack with a large tamiya connector. Also add an extra set of connectors and a little bit of 16 AWG wire to your order, then build an adapter to let you use the battery with your charger.
It's better to light a candle, than to curse the darkness