After wasting an hour contemplating your idea, I'll be the first to say that I think it is impossible to reasonably do what you seem to want to do with VBA. After you have created all of your custom footnotes and were ready to final publish or print your document, then it would probably be possible to take that finalized document and create a list of custom note references at the end of the document, but to do this dynamically while you are working on a document I don't see it happening. Even if it could, it would probably take countless hours to work out and probably take a considerable amount of time to run with each change. Just my opinion.

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Greg Maxey
Please visit my web site at http://www.gregmaxey.com/

Regarding the final output, the total solution is already there. There are very sophisticated pagination programs that handle all the output. And there are many people here that know how to use them very well. But they are not programs that are for writers and content creators. They all work on codes.
The problem is for the content creator who needs the flexibility of a good word processor to create his content keep all notes separately and then deliver it to the the DTP expert.

If you want to see what I am talking about take a look at this. There is one main text in the middle and at least 10 (!!!) sets of "commentaries" i.e notes:

How they did this in the old days by hand is nothing less than a miracle

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