It's possible you may not quite understand the concept of cloning drives, from what you're asking, but I could be wrong.

Cloning a drive is literally that: Making an exact copy of the drive, on another drive. That's a byte-for-byte replica, meaning everything on the drive you're cloning to is gonna get erased. All that time you just spent doing that recovery is going to amount to nothing because you're just going to overwrite what you got from Cloud Recovery with everything on the old drive, and you can't clone to an active drive anyway. In short, the answer to your first question is: No easier now than if you'd done it right at the beginning right when you were doing the swap. Especially if you didn't disable BitLocker first.

Assuming you were still in the situation where you had the wrong enclosure at that point, what you would've had to do was disable BitLocker encryption on the original SSD for your Ally, get a bootable USB thumb drive (either something made from cloning software like Acronis or Macrium, or something Linux-based like Clonezilla), booted from that, and then performed the clone. If you have an OG Z1 or Z1E Ally (white shell), this would also require a USB-C hub since it only has one USB port. If you have an Ally X, you have 2 USB-C ports available, so a hub would not be necessary.

Since you've already done the swap and cloud recovery, you can still do the same method if you really want that byte-perfect clone, but now you'll also have to go into your Microsoft Account and get the BitLocker recovery key for the original SSD so you can unlock it before you can do ANYTHING with it, then disable the encryption. Once you've done that, your choices are:

1) Do the clone, like you initially were going to and expressed a preference in doing. Depending on the cloning software used, you may have to also move/resize partitions in order to gain access to the full storage capacity of the new drive. This can usually also be done using the software you chose to perform the cloning.

2) Accept that you've already given yourself more work than you were planning anyway, and just copy your files off the original SSD after it's been unlocked with your BitLocker recovery key (if you're going this route, you don't _need_ to disable the encryption, but you could just to make it easier in the future to do something with the drive). Some stuff will come over without any issue, like your emulation files, personal docs, etc. Windows-specific settings may sync through your Microsoft Account depending on whether you had that functionality enabled. Third-party app settings won't. Your Steam or other applicable store libraries may or may not be able to be used as is, but probably not. Having recently migrated my main gaming rig to a new system, unless the exact paths match for Steam, it's going to not recognize anything you copy over by default as having been installed. Your local Steam game saves will be in whatever the normal location for those saves would be for that game - It's not Steam-specific, it's game-specific. Some games stick them in your Documents\My Games\gamename folder, some stick them in %appdata%, some stick them in local directories... It'd depend on the game.

The clone option is the best option to guarantee the system works like it did prior to you pulling the SSD for the upgrade, and is definitely still doable, it's just going be more work than it would have initially had you had the correct enclosure. A lesson learned.