I can't imagine we couldn't help you get the gears back in the box in the correct order. Pictures will help.
If you were close enough (mid-Michigan?) I'd be happy to assist getting it back together.
To find another gearbox assembly once Lionel has depleted stock will be a search. You could post a WTB with the stock number. Maybe a derelict for-parts-only opportunity at a flea market/show/meet?
The other option would be to wait for yet another release of this accessory. If the gearbox in question is still part of the mechanicals, there's a good chance Lionel will again have a limited supply of parts available.
As with seemingly everything these days...patient perseverance.
KD