Before anyone says I don’t have enough time to do this in 3 months I’ll be getting the odd flight so I think I can fit it in (plus I’d only be in Brazil and Bolivia briefly in option 2 and would fly between the two)
Well the odd flight will help, of course. Option 2 you can fly from Rio or Sao Paulo to Santa Cruz or La Paz in Bolivia. But it won't be cheap. Flights within SA countries can be cheap, but they charge top price for international flights within SA. I mean backpackers can spend 3 months just going overland from Panama or Costa Rica through to Mexico City, not seeing every part of Central America. It's easy to spend a month going between tourist sites in Mexico south of Mexico City, and ignoring the rest of that country.
So, Charlie, I won't say you don't have enough time to do this, because clocks move differently for everyone. I'll just say you wouldn't see much in 3 months trying to cover this much ground. You'd spend the majority of your days on buses, or going to/from airports, trying to cover this much ground on 2 continents in 3 months.
HOWEVER I am reallllllly worried I’d be going against the travellers route, and worried any people I meet will be travelling the opposite way!
Since almost no one has time to travel overland between Peru/Bolivia and Mexico City, there really is no "travelers route". There are portions of the route that attract a lot of tourists, like the Cusco, Peru to Uyuni, Bolivia gringo trail, which seems to have more tourists going north to south than the other way around.
There really isn't going to a huge difference in the weather for either direction going March to May. The Andes mountains will be drier most places in May than March, except not in Colombia.

