Wow, this is really in-depth! I think I've logged about 3-4 hours and have barely touched all the possibilities. I did discover another issue. I got to the mine, and every attack targets characters in the party and not the enemy. The only attacks I could get to target the enemy were the magical group spells. I tried various keys to move the target, but nothing worked.
*Edit: So, I shut the game down, and the problem resolved itself. I'm not sure what happened, but after restarting, the actual enemies were then targeted in battle rather than the allies.