The issue with modifying the ticket is that the fare for the Capitol Limited has shot up, so he'd have to pay the $200 fare difference for that part of the trip as well.
This is totally false. Please stop making it up as you go because you are giving out false information. Making a change to the Meteor segment has nothing to do with the Capital Limited segment, which would not be touched. An agent who knows what they are doing and following the proper steps can reduce a segment maintaining the existing bucket, which in this case would only touch the Meteor segment. The bus can be added, and the whole trip can be auto repriced in this scenario for the exact same conjunctive fare.
I'm speaking from my experience. When I've tried to modify a reservation that includes multiple trains, I've been told that I have to pay the price difference for the whole thing. And it seems like the OP was told the same thing when he called. Also remember that you'll often get a discount by booking it as a connecting ticket instead of two separate reservations, so how would an agent calculate what the new price would be, had the Capitol Limited fare stayed the same?
Do you really book and modify you're trips? You just turned 16. How do you pay for these trips? And how have you been able to travel them since you were under 16?