If the old system still boots, then you can just boot without the usbmlc plugin and use SaveMii Process Mod to backup your saves.
For the apps no longer available at the eShop, you can copy them to the USB storage and hope they aren't corrupted.
First install your games fro. The eShop, as you won't be able to access the eShop with Pretendo. Then setup Pretendo, which requires a second user. And once you have that look after your saves, so you can restore them to the correct user.
Did you use SaveMii Process mod?
What you did so far ist correct, but you are missing the part where you download and install the system titles. The USBMLC guide has a section for that. "Rebuilding MLC"
If you have a USB device connected, disconnect that, as it seems to have problems.
I also see errors, which look like a bad bluetooth module, that could cause the freeze.
There is nothing pointing to the eMMC being bad. The eMMC is not your problem.
the SD emulation is only active inside the Wii U OS. In minute it uses the real SD card. Save Mii, since it runs in the Wii U OS, it uses the emulated SD.
vWii works like normal. It isn't affected by the SD emulation, most Wii Homebrew supports USB nativly.
If you use a USB loader, that would...
No, you can still do that. The SD works the same in minute for unbricking. The SD emulation only affects IOSU.
USBMLC also doesn't care if it gets loaded form SD or SLC or if you have SD emulation
I will just ignore the AI part.
Check if the console works without the SD card in. If not install ISFShax and dump the logs in minute (Backup and Restore -> Dump sys crash logs). Zip the whole folder and share it here.
If you have wii motes or a pro controller check if that works.
If you don't want to keep the SD permanently in the console, consider to partition the HDD. With the SD emulation version of the plugin, you can use a partition on the HDD as SD for homebrew. You would need to do that beofre setting up USBMLC. The USBMLC guide should link the the USB Partition...