You need to be aware that ordinarily passengers coming by train from France into Italy need to switch trains in Ventimiglia, and the last time I did that (two weeks ago), I noticed that a large number of police are in the station asking travelers to show documents. I also saw police getting on and off trains between Nice and the French border. They mainly seem to ask young people who look like they are from third world countries, although those were only my brief observations.

Well, there can be consequences to those violations - like being barred from entering the EU for a good while. Do some more research to determine if the consequences are worth it because you will be busted, in all likelihood, leaving the EU.

'I fully understand that overstaying my visa is against the EU regulations so please I am only looking for advice on what's the best route from Spain to Italy by train.'

So you are asking for contributors to be complicit?

My advice is to come back to the US at the end of your visa and then plan another trip to Italy legally. You do realize that If you ever travel back to Europe, you could be scrutinized more because of overstaying dates in passport.