How to type characters for phonetic guide over a word in Microsoft Word?

You could potentially use a table with the column width set to autosize. Put one character in each column. Not sure you can make it work, and still tedious, though less so.

Otherwise you'd need some sort of tool that could read the font metrics of the second line and space the first line accordingly. I have no idea how you'd go about this, though. Likely some external process would be more likely to succeed than doing it inside Word.