Alright, I should be able to fix that first thing in a bit. Not sure where the option went wrong, but shouldn't be too much trouble to re-implement it entirely, if I have to.
Your second thing is going to be a lot trickier to figure out.
Generally speaking, dual wielding, or two-handing weapons should not impact the third equipment slot at all. The whole system was hard coded to use only slots 0 and 1 (the weapon and the shield slot). Slot 1 also becomes the second weapon slot when an actor is dual wield type.
My first question, is are you making your actors dual wield type? I only ask this because you've already mentioned that you're using equip core to make certain classes have different equip slot types, and it's not a reach to say that maybe you've given your dual wield classes two weapon slots instead of setting them as dual wield type. If this is the case, you're also not the first person I'm aware of to do it this way either. The correct way is to add the below trait to a class.
The reason I want to verify the above is because if you are just adding a second weapon slot to your dual wield actors, it might explain some of the weird behavior regarding two-handed weapons you're describing. Let me know, ok?
Secondly, I want you to turn off the optimize equips on job change plugin entirely, and then change classes and tell me what happens. The default behavior for the class change plugin is to unequip any items that cannot be equipped by the new class when changing classes. I suspect that without the optimization added by this plugin, it might still be removing slot 3 for some reason. Please verify and get back to me.
Thanks.