As calibre can read an OPF file that is supplied with the book, maybe the way to go is to generate that. I'm pretty sure this doesn't need the manifest and spine, so it would be relatively simple. The OPF can include custom columns, so adding an original file name that way would work.
The other thing is that it sounds like the attachment id could be used as an identifier. Storing it as an identifier and creating a MobileRead metadata source plugin would allow easy navigation back to the source. And the metadata source plugin doesn't have to have search capabilities. It just needs to translate the identifier into a display string and a URL.
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