In a effort to get my domain un-blacklisted, I have deleted many of the files shown by https://www.virustotal.com/#/domain/dw3i9sxi97owk.cloudfront.net - They should now return a 403. I noticed virustotal only lists 100 files, so I wonder if there are more but I can only see the last 100? Although I noticed the files go back to 2017-12-03 which seems a large enough timeframe.
I noticed some of the files are only marked as malware by 1 engine, "Yandex Safebrowsing". I'm thinking maybe this engine has a very low threshold and might be marking my files simply because of the domain, not the actual contents. That's just a guess though. An example is https://www.virustotal.com/#/url/bce81cd104b72a1451467febd87641abddf3e849c00188e2d2622ab4200559f2/detection
We scan the files using ClamAV free version - it seems it does not detect malware as well as some other products. Shame.
@Zynthesist - Please can you let me know if more is required from me? Thank you for your help so far.