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These threads are helpful:
For your script it looks like you can create some kind of customized ScriptUI input box in which you can assign what characters or words get some graphic style - or manually styled via script by changing the baselineShift property of a characterAttributes of a textRange. Here's an example:
var doc = app.activeDocument;
var t = doc.textFrames;
alert(t.characters.characterAttributes.baselineShift); // 0 - no superscript
alert(t.characters.characterAttributes.baselineShift); // 3 - superscript is at 3 units
Wow that looks super useful!
Wow thank you all for your input and help! I definitely think what has been said will aide me. Will have to dive into it later this week and see what I can do.