I agree that the Altiplano is the easy part. The problem is the costal range that borders Lima. Lima is important as the gateway to the country and where both the government and a lot of people are.
I should have been more clear. I referred to the colonial times. In any case, you dont need the connections just for the sake of exporting from source. You need to send the materia to cities for production, and you need those cities connected between themselves.
You also have to think how easily people moves from one region to another. Industry means mass movements and those need either rivers or railroads, let alone a port if you want immigrants.
I still beg to differ. A railway that connects the Altiplano with Mollendo or Ilo already has an outlet to the sea, to export raw materials, it’s not too difficult to make said railroad go north from there, all the way to Lima, since the terrain is much, much easier. But let’s look at production.
Centralization of the means of production in Lima is a mid to late 20th century phenomenon. Arguably, to this day Bolivia is more decentralized, as La Paz hasn’t attained comparable levels of centralization. Thus at the dawn of independence you had textile factories in Cusco, wine (and pisco) making plantations in Ica, mines in Arequipa, and a buoyant trade hub in Ayacucho. Further north, you had large sugar and cotton plantations, and whaling stations on the coast. In Bolivia, you had quinine fields, vast agricultural production and, of course, mines.
Forward to OTL mid-19th century. In addition to the enterprises mentioned above, you have the rise of textile factories (relying on wool) throughout southern Peru, and the creation of foundries, and even an armory in central Peru. In Callao, right off of Lima itself there was a fully functional naval shipyard.
Thus, with a nation (Peru-Bolivia) that has its center in the heartland of the country, not Lima, you have a number of opportunities to push for development all over: Paita, Callao, Arica, and Cobija where all declared as open ports during the Peru-Bolivian Confederation. Railroad networks linking all of those ports along the coast isn’t hard (but again, we go back to corruption and mismanagement to deal with.)
Roads can link the main cities in the highlands (as they did since Pre-Colombian times) until viable railroads can be established. And from the headwaters of the rivers watering the rain forest, riverine causeways can be used to explore and colonize the East (as it was done OTL, but much later.)
The key here, is to have the political center in the highlands. Unlikely given Lima’s historical hold over Peru, but not impossible with the right POD.