I downloaded the sample and looked through it. The HTML is abysmal and has a ton of unclosed anchors, which I'm assuming is what's causing the recursion problem. In the conversion dialog, go to the "Search & Replace" tab and add two expressions.
This first one takes care of the unclosed anchors causing the crash. In "Search Regular Expression", copy or type the following:
Code:
(<a id="filepos[0-9]+">)
Then in "Replacement Text", copy or type:
Then hit the "Add" button.
Now for the second one. This one fixes some broken superscripting around footnotes. In "Search Regular Expression", put:
Code:
<sup/></a><a (href="#[^"]+")>
In "Replacement Text", put:
Code:
<a style="vertical-align:super;font-size:.75em" \1>
Now hit the "Add" button and then the "OK" button to run the conversion.
When I do that for the sample, I end up with an epub that looks reasonably like the mobi sample. Hopefully it works for you. If it still looks wrong on the Kobo, let us know and we can probably tweak the expressions. In particular, check the font size on the footnote links (compare note "a" in Genesis 1:1 with note "e" in Genesis 1:16 to make sure that the "a" and "e" look the same). The ".75em" above will apply to the "e" and means 75% of the normal font size, so you may need to make it a little bigger or smaller so that it matches the normal superscript size.