No, you can charge them separately, but most prefer to charge them 'as one battery' in series (so it becomes a 4 cell). A custom balance lead would need to be made, but it's not that difficult. The only reason that people like to charge two at once is that two are required for the car at once. The charger cuts the Lipo charge off when the cells reach capacity, so it doesn't matter if you charge them separately. Even if they are both connected, the charging stops when one cell reaches full voltage, and the charger enters balance mode to bring the other cells up to the peak voltage. Therefore it is irrelevant whether you charge them at the same time or separately.
I can't see why using two Lipos of different ages is a problem, so long as they are the same cells (so have the same capacity and discharge rating (C)) there shouldn't be a problem. Unless one is completely knackered of course and the other is brand new or something. A couple of cycles different won't be a problem though.
4mm connectors are enough to run 1/8 Brushless. It's only when people run them in really high power applications that they start to really heat up and efficiency is lost.
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