I fully understand that if I had left my character on 1.0, the transition to 2.0 would have broken things. However, I already went through that way back when 2.0 was released. I had my WHM, but all my stuff was reworked for 2.0.

That's fine.

I played through much of the game's main story and specific job quests after that transition, however. THEN I deactivated my character. Reactivating it now, however, I should not have things this screwed up again. I left off at 2.x, main story quest line and job quests significantly advanced. So now, why would it be messed up?