As you said, you need to filter at least the known sets out. I've never used RomVault but it should be easy to use, you just have to try it some times. I guess the best / easiest way of doing it is to download romvault and the last tosec dats from romvault site (so they came in the right structure), just put all your sets (or a copy of them) in the ToSort folder and do a scan/rebuild (as i said i don't know how it is named). Alternatively you can use clrmame pro but i would say it is a bit less user-friendly (although easy to use) and you need to scan/rebuild all amiga dats one by one or learn how to use the batch scanner/rebuild.
All these tools use the information contained in datfiles to identify sets - crc32, md5 or sha1, and rename them accordingly, they do not identify files based on file names.
Once you've done that all known sets will be moved to the respective Company\System\Categories*\ folder (eg. Commodore\Amiga\Games\[ADF]\), the ones that were not recognized will still be at ToSort (i think) and those are the ones that matter.
If those are still too many to upload to a fileshare site or if you just prefer using other method, please contact me.
As a final note, since we already identify a lot of amiga stuff you will probably discover that most of the unrenamed files are probably just some alternates made unintentionally by someone over the time, something that is boring and not really interesting to add but i hope you can find some good new/unrenamed sets too
Currently in TOSEC, our member mai is the maintainer for some Amiga dats (especially the huge amiga - games - [adf] one, you might want to talk with him first about it. Make sure you know / read the TNC well too to gain essential knowledge on how to rename the sets and good luck
The only ones so far that I was unable to locate in any dats (of course I could have missed them) are:
Syzygy v2.0 (1992)(Johnson, Keith)(SW)[AMOS]
UChess v2.18(030) (199x)(Uzan, Roger)(AGA)(PD)
The first one exists in various sets but only for other systems, as for the 2nd you can find these files:
UChess v2.01 (1994)(Uzan, Roger)(AGA)(PD)
UChess v2.04 (1992-12-16)(Uzun, R.)(PD)[h Extreme][WB]
UChess v2.88 (1994)(Uzan, Roger)(AGA)(PD)
UChess v2.88 (1994)(Uzan, Roger)(AGA)(PD)[a]
in "Commodore Amiga - Games - Public Domain - [ADF]", since i'm looking at a newer dat (WIP) they might have been added after the last release