Hi Jim
There's no 'tolerance' persay, just that sufficient space is required for the truck to swing freely. More important is that the couplers of your cars are all at the same height. Because manufacturers have their own designs which always seem to be different, you may need to add washers to some cars, and trim some material off others to get them right - if trimming material off is too hard, add shims to the couplers to make them lower. This is where a coupler gauge is very handy....being the complete tightwad that I am, I make my own from blocks of wood cut to match Kadee's standards.
I'm a complete greenhorn when it comes to replacing axles (I prefer to swap the whole truck, too hard to buy spare wheelsets where I live) but the key dimension here is overall length of the axle, followed by whether it has pointed or shouldered ends. NorthWest ShortLine specify this for their replacement wheelsets, and I seem to recall they also say what brands some sizes are for.
Regards
Paul
Whangarei, NZ