Have you tried to start from scratch and repriced your revised itinerary from the beginning? You might be better off to just cancel the current tickets and apply them as credit towards the new tickets, minus the change fees.

Based on your description of the options given to you, IMO the agent gave you bad information. Call back and ask the next agent to rebook segment 1 (even though you’re not changing it), and I can almost guarantee that it will return a lower fare.