Disk3 having the same UUID as disk2 can't be a coincidence, so something happened there, only possible recovery option would probably be a file recovery util.
The one from /mnt/user and /mnt/disk3 is the same file, if the current one is empty worth trying the backup one, just copy over it, but first disable VM service.
Yes.
It's difficult to say, it could get better, it could get worse, one thing you can do is to clone the that disk with ddrescue after the parity is built, if no errors great, if there are errors you can find out which files are affected.
Do you mean it was also slow transferring from a USB device? And it was USB 3.0? Since you don't have parity try a transfer form one array disk to the other, you can do that with Windows after enabling disk shares ( Settings -> Global Share Settings), note only transfer from a disk share to another disk share.
Feb 23 15:16:40 HakkaFarm kernel: XFS (md3): Filesystem has duplicate UUID 7ef05469-45c6-4921-be50-a5c727615728 - can't mount
This is why it's not mounting, post output of blkid
I also have a few HDD based raid pools, and depending on what you're going to use them performance can be good, like for reading or writing large files, it's just never has good as an SSD for IOPS.
That's expected, once a disk is disable it needs to be rebuilt., disk itself looks OK, emulated disk is mounting and if data looks correct you can rebuild on top, I would still recommend replacing/swapping the cables to rule them out before rebuilding.
This should help, but note that vdisks are not in SI units, so it's allocated 1TiB while the disk is only 1TB, and not a good idea to create a vdisk larger than the available space.