[slowsmile]

I had the same superscript sizing and spacial problem as you -- it seems superscript derived from a Word doc are unable to automatically use the default font in either EPUB or Kindle but Word handles superscript inherently. Also strange is that the Word HTML Filtered version also cannot handle superscript properly from the original Word doc -- always ends up in 1 em size(12pt) with disturbed line spacing.

Therefore you have to re-declare font-size and re-adjust vertical-align in your superscript span char style declaration in EPUB -- then it comes out fine in KIndle;

Here is how I changed the superscript declaration in EPUB HTML and got it to work:

span.SUPERSCRIPTRef {
font-family : Arial, sans-serif;
font-weight : bold;
font-style : normal;
font-size:0.60em;
vertical-align:top;
color :#c06400;
}

You may have to alter some of the above to your own needs but the above declaration works fine in EPUB and on Kindle conversion. Beware also that if you change the font-size to 0.8em or greater -- then this starts to disturb line spacing.

Haven't tested it yet on Apple, but I reckon that it should work ok.