This route, as mapped, follows the current railway line although Twain took a "barouche" from Lecco to Bergamo.  This should provide a good approximation of the road traveled

The first section of the line is the Milan–Monza line, which was opened by the Kingdom of Lombardy-Venetia (part of the Austrian Empire) as the Imperiale Regia Privilegiata Strada Ferrata da Milano a Monza ("Imperial Royal Privileged Railway from Milan to Monza") on 18 August 1840, the second railway opened in 

The Genoa–Milan railway is a major Italian rail line, connecting the cities of Genoa and Milan. It is 157 km (98 mi) long and fully electrified at 3,000 V DC. Passenger traffic is managed by Trenitalia.