Upgrade to Windows 8 and use Windows desktop search, its light years of the one that runs on XP, which from memory was on the wrong side of useless
My main library is also academic and similar papers - WDS works like a dream. It finds things in my calibre folder faster than calibre, but so it should;
its database is proprietary and optimised for Windows NTFS and search.
On XP you could try using the Google or Copernic tools, if they still exist. IMO the best searcher on XP was the one from Yahoo. But, they discontinued it; maybe MS snaffled it and folded into their current WDS.
It would not be 'very hard' to integrate Calibre with Windows Search on Vista/7/8. If Apple expose an API for Spotlight then it may not be 'very hard' to integrate Calibre with it. I'm not sure what one would do regarding linux - Recoll is a possibility, but its not vanilla linux and it may not run on all variants.
But to do all three may be 'very hard', be considerable work as one would probably want to rationalise them into some common shape - almost inevitably that will mean trade-offs and lcd compromises. Then comes the problem of supporting different versions and features even within the same product - some vendors pay more attention to backward compatibility than others do.
AFAIK there's no WDS iFilter for ePUB, so I convert them to RTF and Windows indexes those, there are several iFilters for PDF's. Spotlight will index ePubs and other eBook formats via an add on, as will Recoll, also via an add on.
A major advantage of OS indexing and search is that it will get other things, like emails, presentations, correspondence, spreadsheets, blog posts etc. For me that's invaluable - more or less a must have.
Another is that it avoids the problem of over tagging. Example: 'round-trip banking' has become one of the 'in phrases' since Krugman used it in the NYT last week, I don't have it as a tag in Calibre. But in less than a couple of seconds, WDS turned up 19 relevant documents (12 in my Calibre library, 3 emails, 2 spreadsheets & 2 blog/media comments).
BTW - I access WDS most often via xplorer2 Ultimate Edition, its my normal file manager; this demonstrates WDS can be integrated with 3rd party products.
But asking Calibre to integrate itself with these OS level tools is a very big ask, its hard enough keeping up with the vagaries of different file systems on different platforms - throw platform dependent search indexers into the mix and you're into OMG territory
BR
Just watch, it'll turn up in 0.9.30 and I'll have egg on my face - again