lol, there are no silly questions... well, there are, but we won't go there.

So, no need to jump off any bridges...
Anyway, high temps on a connector and/or wire means there is a voltage drop. The amount of drop depends on the current flow and the resistance of the connector/wire. This voltage drop means the balancer will see less voltage than there actually is on the cell and may balance according to that erroneous reading.
Hot connectors are obviously bad and should be replaced with something with less contact resistance. Mini power-poles, mini-deans, etc can work - whatever you use, you probably want something physically small. Even though wires don't get hot, they could also be dropping voltage, but because they are fairly long, the resulting heat could be being wicked away. You could measure the drop with a meter (measure the voltage at the extreme ends of the wire). Remember, balancers are trying to maintain cell balance to around
0.05v, so ANY voltage loss can trick the balancers.
That said, if you want to charge and balance through the taps and don't want to replace all the wiring, I would make those balancer wires as short as possible. Wire has X amount of resistance
per foot. So, it stands to reason that if the wire is shorter, there is less resistance.
So, go with good connectors that offer low contact resistance and at least 7-10A rating (higher is better even if you don't charge that high) and keep wires short.
Oh, since the charger charges at 1C no matter what, you can probably trick the charger into charging at lower rates by telling it that you are charging a lower capacity pack. So, if you want to charge a 2000mAh pack at 1A, set the capacity to 1000mAh. Just be aware that this will take twice as long and the charger may have a safety timer built-in to terminate the charge after X amount of minutes...