Dave,
Height of the boxes are more dictated by the width of the stock that I have on hand. Normally anywhere between 4-8". For the most part I use full 4/4 stock and use 5 thicknesses for a 'depth' of just under 5". Bookmatching pieces can bring out some interesting patterns on the tops of the boxes.
Width is based on the pattern and proportions used for the hieght of the box, if your wife has other bear figures around -- it should be fairly easy to get good proportions from one of those.