Not familiar with arq spec, but if you have the bandwidth to download and store the files, then hashdeep[1] can do the audit for you.
Basically generate a hashdeep file using the command "hashdeeep -rl $dir > $dir.hashdeep"
Then on the directory you want to verify, run the command "hashdeep -avvk $dir.hashdeep -rl $dir"
It should be doable with something like hashdeep, but I would strongly advise against it.
If your MFT routinely gets corrupted, then some of your actual data probably also gets corrupted routinely. MFT corruption is only one type of data loss, and a very narrow one at that.
A question for you: what's your plan if a drive dies? Not as in corrupted MFT, but as in drive is completely dead.
Drives dying is not a matter of "if", but a matter of "when".
What you need is an actual backup, but short of that, you would probably want a storage system which offers redundancy and built in checksums.
If you want to stick to Windows, you should take a look at SnapRaid. It will allow you to spread your data across many disks, and use one or two disks for parity. This parity along with the built in checksums will automatically detect corrupted data, and restore the data from the parity. It will protect you from bad sectors, bit-rot and even whole disk failures.
It will however not protect your data if more than the amount of parity disks are lost. So if you have a single disk parity, and you lose two disks simultaneously, you have lost your data. With a two disk parity you would be protected against two disks failing simultaneously. If even offers snapshots, which can protect you from accidental file deletion.
SnapRaid will however not protect you from disasters like a flood, house fires, lightning strikes frying the system or of course theft. That is why people constantly reiterate that RAID is not a backup.
hashdeep is the latest addition to my arsenal.
It is not for downloading things (I like those tools too of course) but to store and manage simple plain-text lists of hashes of all files in the hoard, to be able to notice if a file has gone missing, or something broke. Also great for scanning old disks to see if they contain files that are not yet added to the hoard. I have too many unsorted old hard disks and optical disks that I now finally have a good tool to scan.
Great thing is that it runs on all platforms. Download an installer for Windows or just install it using a Linux/OSX package manager. And the source code is very basic C++ with no external dependencies. It seems very likely that this tool, and the files it generates, will be useful for as long as my hoard lives, so that no matter what file systems and storage types I move files between I can run an audit to confirm that all files still matches their original hashes.
The problem with Baron Replays is that they link to a different VirusTotal link than the current download. The one they linked to from their download page had a different SHA than the download link, which makes them less trustworthy. Also, the actual download link shows 3 different trojans, one from trend micro - https://www.virustotal.com/en/file/6046e68c4c24a4de1132b61e9b8217fb3d3610c9a88906aa18abc5cf447a2fae/analysis/ vs https://www.virustotal.com/en/file/6f934a3b81d460a4739fd49a9caf0228c0c9b90bb9f353f4d9ea8a30e3cc6864/analysis/1406400808/ edit - sha256 calculations based on https://github.com/jessek/hashdeep/releases