Step 1:
Create virtual hard drive with Disk Manager in Windows.
Doesn't matter what format, just make sure its 1GiB or more.
Step 2:
Mount the virtual hard drive .vhd file you just created.
Step 3:
Download and run
https://rufus.ie/
Then use it to format the mounted virtual hard drive.
Format to fat32 32kb clusters.
Step 4:
Add the files you want to work with to the virtual hard drive.
Step 5:
Unmount the virtual hard drive
Step 6:
Launch PCSX2, go to controller settings, and add a mass storage device as the .vhd file (Your virtual hard drive is going to be PCSX2's USB)
Step 7:
In memory card settings, enable and create a "folder memory card"
Step 8:
You now have the ability to add files directly to or from PCSX2's USB and Memory Card.
Proceed with your desired tasks, utilizing Memory Card Annihilator and wLaunchELF within PCSX2, and File Explorer within Windows.
Once you have restored your mc image from PCSX2 USB to PCSX2 Memory Card, you can then add freely or remove freely any files to the "Folder Memory Card"
Once everything is to your liking, you will simply run MCA again on PCSX2 and make a backup image of your PCSX2 Folder Memory Card. Once you've done that, you'll find the new image inside the .vhd file when mounted in windows explorer.
Ta-da!