You could try installing the Microsoft Word table format plugin and export the questions to Word format. This format omits the question IDs so that particular issue would be avoided. In addition, the XML export question order could be quite different for each category, but in Word you could sort the questions by name (each name is a Heading 2 style) to avoid this issue too.
Word has quite a good compare function so the comparison results are very good, exactly highlighting changed words, not just changed lines.
If you do use regexp to remove question IDs from the XML files, the best text file comparison tool I have found comes with the Total Commander file explorer. Like Word, it does word-by-word comparison within lines, but the feature I like best is that you can re-synchronise the line comparison. For example, if there is one extra question near the start of one file that throws out the whole comparison, you can manually tell it to re-align on the next question and start comparing again. I find this is quite a typical scenario for XML and HTML files.