How do I get the trains running in the Warren?
There are some side missions in each district, which free the district of enemies and activate certain things like trains. I think the missions to re-activate the trains are called 'El Train'. They should be fairly easy to find, if I remember correctly (it's been a while) when you're in the area you should see a mission marker on your map. Follow that, complete the mission and the trains should be running.
Or, you can ask your boyfriend how he did it :)
btw, +1 for doing the (cooler) Evil playthrough!