<p>Is there any software to help in learning / understanding / experimenting with the rules of harmony and counterpoint?</p>

While very carefully coded applications could give you some hints, I find that the most important lesson is when to break the rules. And a computer program could never help with that.
I suggest you buy a book instead. Good ones include
The style of Palestrina and the dissonance
Twentieth century harmony
I haven't read any English books on baroque, wiener or romantic style.