Unfortunate news, I still haven't resolved the quest problem.

I thought I figured it out, I must be very close. I managed to get the game to remember repeated quests, but after a second reload it will forget them once more.

I'm trying to not write my own methods for saving this information since whenever KisSoft updates the game, I want the mod to remain as compatible as possible to future changes, as I'm sure there will be many.
The downside is that I'll hit walls like this one where the solution isn't immediately apparent.
I guess I'll just need another day.