I have the same problem. I think the whole mission package is overcomplicated.

same here

In Mats Missions your task is not only to fulfill “his” aims, first of all you have to get your economics straight. All of your spendings have to get you a revenue soon, all of your lines should be profitable. So don’t make any expenses you don’t essentially need: Stations just as long as necessary. Inner city transport in Sao Paulo? Will probably just get stuck in the traffic and never earn money so skip that. But I am learning by replaying the mission right now (and having lost the money cheat): When you want to embark passengers on a cargo port you don’t need a passenger building, a pier is enough. And you can even save on ports as well as station by configuring just after construction and bulldozing any unneeded parts to redeem some money.
In this Sao Paulo mission it is hard to get the Naples food line profitable. I chose to connect the Ischia fishing industry by ship to Pozzuoli and Naples. But the ship only half loads with fish and food (I am not sure whether by purpose or bug). But you don’t get enough income when only half the ship is catered. So you have to transport passengers as well. But it seems fish and other cargo are just loaded on the front half of the ship – and if there is already just one passenger on board, no cargo at all will be accepted. So you have to really plan your line: First get the fish loaded, then accept passengers on the second half. And if in Naples all food is disembarked, a passenger heading for Pozzuoli might get on board the front half, again barring to restock fish in Ischia … it is a really hard work to get everything running. But I like the challenge now I better understand it.