The boss is really unexpected, I would say make a warning pop up to save. You could set a choice event. (There is a boss near by, would you like to save before continuing? ) That would help prepare for the event ahead. And, I also didn't save first time around, so I had to play from the start again.
I did equip Yumi with her weapon this time around which I didn't realise before, but the boss has got quite allot of HP. I heal about every two turns. Maybe bring that down the boss HP to around 2000 and lower the power of quake. Should be great after that.