Starting off with basic ideas for the armoured train, and in particular what sort of engine it should have (Warning, large picture)
Since the train is supposed to be relatively old, I think a steam engine is the most appropriate - it also plays up the strengths of doing the vehicles in CG; you can do all the complicated valve gear and other reciprocating gubbins without sending the animators mad. Plus, steam engines just look cooler than more modern designs.
Taking the top right design as a base, I thought I'd explore the possibilities of armouring it
Middle - Armour straight from the factory
Bottom - Armour after someone has spent a couple of months having to lift the access panels every day for maintainance