The most popular programs to convert to LRF are Calibre and Book Designer. Both will handle footnotes.
There's a Calibre section on the forum. Calibre is an extremely versatile program.
And here's a link to the Book Designer entry in the wiki:
https://wiki.mobileread.com/wiki/Book_Designer
(Also download HarryT's Book designer tutorial for advice on how to make links. There's a link on the wiki page.)