That is rare enough to make me question if it's worth adding as an option... (See this popular thread http://forums.adobe.com/message/4273659#4273659 for a number of more often requested improvements -- it's "popular" under ID *users*, not Adobe itself).
If you do need this wacky scheme as actual footnotes, you could delete the generated note number from the note itself and replace it with a manual cross-reference. Insert a link to the cross-reference into the text in the right place, where the footnot number is. Then you have to "hide" the actual footnote number in the text -- you cannot *delete* it, of course. Change the character style for the note number to color [None] and a size of 0.1 pt.
There is absolutely *nothing* you can do to make footnotes appear at the bottom in any other order than they appear in the text. You have to manually move the footnote markers around until they appear as you want it.
I'm not sure cross-references do the job for you. My experience with footnotes are limited to the *usual* problems.
Does your footnote scheme have a name? Honestly, it doesn't sound like anything I've seen before.
Normally I would suggest just adding a superscript number instead of an actual footnote marker for all but the first instance of each note, but the whole things seems so whacky that I suspect the best bet is to create the notes first (probably as end notes, not real footnotes) and, as Jongware suggests, use cross-refs, or just add manual superscripts in the body.