Good job! I'll try the game right now. Just out of curiosity, what was the problem that made the game freeze?
It's quite embarrassing actually! I had an event on the map I left for testing the end scene, which bypassed the final battle. When I read about your bugs, I kept looking in the wrong spot (I'd check all the events and dialogue for Ruffus etc).
As for winning the boss battle, what level are your characters, what items do you have, and what skills are you using? In my personal play-through I thought the battles were a good challenge level. I leveled blue fish to 8 and had him alive for the boss battle, not only so I had an extra meat shield, but because he has the best debuffs in the game. In two full playthroughs for the final version, I built:
Black Cat - Pure damage and crit. (Sniper rifle, magnifying glass, etc)
Brown Dog - Balanced (Some magic for his heal, some damage, some tankiness)
Yellow Duck - Pure magic for his life drain + magic skills I bought from Rusty in the city
Blue Fish - Life steal / regeneration (trolls heart)
And in my second play-through:
Black Cat - Pure magic (huge laser beams all day)
Brown Dog - Pure attack damage
Yellow Duck - Mostly attack damage
Blue Fish - Tankiness (so I could keep him alive for his debuffs)