Do you refer to the EPIC 3000 mAh batteries?

Tower does not give technical specs on these cells, so it's hard to say if they're any good.
These cells are probably what's left, after the good cells are selected, so take care not to overcharge or drain them excessively, or the weakest cell(s) will die.

If you want to spend the money, try the GP3300 SCHR-U cells (Pushed & Matched), you'll be amazed...

Temperature: NiMH's are supposed to go hand warm into the boat, preferably fresh from the charger, charging them the day before running them is damaging to the cells (to say the least...).
You should be able to charge them with 3A, using a Delta Peak charger.

As far as I know, a bad pack can't damage the ESC.

Good to hear Tower is sending you a new ESC.

Another unwanted source of heat are the Tamiya connectors, replace them with goldplated connectors like Deans, when the Tamyia's have started to corrode, you'll have instant improvement.

Regards, Jan.

Just make sure, the heat from the packs can't get to the ESC directly.