Thanks again, Idolse. I appreciate you taking the time to respond. But I'm afraid we are going to have to agree to disagree on your suggestions.
I used to dabble in website design, and have become quite rigid about the importance of having the HTML validate. It may well be that putting the text directly in a blockquote without paragraph tabs would make it indent for mobi ebooks. But it certainly wouldn't validate, and very likely would not work for ePubs anyway.
So far as the <sup> tags are concerned the whole point of my efforts in styling the footnote numbers was to make sure that they did not project above the other characters and force a wider line space. Even if <sup> is legal I didn't use it for that reason. My objection to what calibre did is that it over rode my styling, and imposed a style of its own whose result is ugly.
Similarly, I'm not that fussed about what what font appears in the book. But I am annoyed that calibre ignored what I went to some trouble to style. It may be that I am asking things of calibre which it isn't designed to do.
Your suggestion about the debug option is worth thinking about, but given that the HTML worked for ePub I'm reluctant to dumb it down just for mobi.
Thanks again for your help, Alex