[cybmole]

links followed by text is what I'd expect to see in an ebook,

is the article text neatly formatted ? if so, then what is the issue exactly - waht other formatting are you trying to preserve?

as a comparative test, try emailing the html as an attachment to your free kindle address & let amazon convert it and wi-fi it to your kindle.

compare that with the calibre output.

also try open the html file with MS word & see how it looks in word.
you can, in word, delete any unwanted stuff then save it as html before adding it to calibre.

maybe you could post an example, as an attachment, if these are publicly available web articles