I have Bunny stacking fairly well on the table but I do not know how to encourage a free stack.  Pretty much if you produce a ball you have her 100% attention - however!!! I taught her to sit before we toss a toy as she would jump in your face to get you to throw it or jump up and grab the toy from your hand (rude behaviour lol) .. making her sit stopped this behaviour but now that I am trying to get her to stack - if I show her the ball she sits AND on the same note.. she is trained to  sit and wait for "okay" before eating because she would rush in and try to conquer the bowl while you where still getting food in it.  Making her sit and wait stopped that behavior..   I sure didnt think it through did I. 

Any suggestions on other methods of encouraging free stacking?

Have you tried using a "bait" type treat as a reward? I have taught Spanky just like you have Bunny (I'm glad to see someone else training their dog manners)

I would start her out using a leash and giving her the "stand" comand, (you may have to back up a few steps to get her to stay standing or place her in the standing position) to start out with and when she stands praise her & give her the "bait" treat, only use that treat when working on this comand,she should start to put 2 n 2 together after a time or two. 

Spanky will free stack all day long, he's quite proud of himself  I use either a treat or a small sqeaky toy that fits just in the palm of my hand. I hope this helps..keep us posted