Model train controller

[ppppenguin]

So a 5 amp diode in circuit with each rectifier should protect the regulator, in the event of a high positive voltage being connected to the output.
Something like this;

But what about the case of a short circuit over current, how can the rectifier be protected.

The rectifier should be able to look after itself. Just uprate it a bit if necessary. An inverse diode across the output of each regulator will protect from reverse voltages.

Are you trying to protect against transients or a sustained fault? The diodes should protect against transients without any trouble at all. A sustained fault needs a fuse for protectin. Either conventional or polyswitch.