I painted as if it was fresh from the workshop. While the wagon runs well a number of you suggested that in reality they wouldn't look new for very long. My solution to this was to print multiple wagons so I could have sets representing them at different ages and amounts of abuse. I even got as far as experimenting with how I would paint older looking wood but I never got around to actually painting another set of models.
Well I still haven't painted a set, but I have painted one which you can see here alongside one of the original freshly built versions. My approach followed the second of the two approaches I experimented with for the wooden sections. The metalwork was painted black then dry brushed with a little Model Color London Grey (#70.836) and Rail Match Dark Rust. The final touch was a little bit of Flory Models rust weathering wash before a waft of matt varnish was applied to seal everything in place. I'll add the couplings at some point but even without them I'm really happy with how this all turned out. It definitely looks older and more well used without looking badly abused.
If you fancy painting one of these yourself then head on over to Penistone Railway Works and I'll happily sell you some.