I beat the boss I was stuck on. For anyone that gets to the same point, here's the strategy I used:
First grind on those (somewhat tough) soldiers until you have Gafka to level 28 or higher. Use a party of Stocke, Gafka, and whoever else you want, but you'll probably want someone that won't die easily, which is why I used Rosch. When you fight the general, have Gafka use the skill he learned at level 28 (it's called Nigwog Wave or something very close to that) every turn. It hits the middle row, which the general is always in, and it's ridiculously overpowered. Have Stocke use Power Wave to take down a Clockwork Thunder every turn, to minimize the damage they can do. If everyone's at decent health have Rosch do the same with a move like Burn Knuckle, but if not, have him use healing items as needed. Don't bother having Stocke or Rosch attack the Clockwork Thunder in the middle row, because Gafka's attack is going to destroy it anyway. Just keep doing this, and the general will go down. The battle actually got pretty easy, with my characters moving just fast enough to destroy all three Clockwork Thunders and force the general to waste his turn calling more.