I am confused about how to rotate a circuit. If I copy or attempt to lay down a template, the output#1 is always on the lower left. So if I have to orient all the elements differently (in this case a train stop), all of the I/O ends up in the wrong place. Is there something I am doing wrong?

+1 for that.

So for the trains, I ended up just making 4 copies of each blueprint with the circuit modified for the proper direction of the station. It works and the stations look so nice now.

I was thinking about making the train controller listen on all possible inputs and deciding which to use at runtime based on the unique control signal...

I've found that you CAN actually have multiple poles with the same name & ID, they have their signals mirrored (for input) or stacked (for output). This may be useful in designs like this.

The rotation of a blueprint should be ok, now.