Something is wrong with how you created the Qtfiles64 folder because it should have been populated with the needed files automatically. Check these steps:
1. Be sure the makeportable2.cmd file's content match those on the website and that both that file and the file "iTunes64Setup.exe" are in the same folder--best to just create an empty folder and then put only those two in it.
2. Now run the makeportable2.cmd in that folder--a command window will open up while it runs, and there may be a long pause at one point after a message like "Everything looks OK!"--do NOT exit the command window then, just wait a while and you will see the process eventually continue on its own, and it will close the window on its own when it is finished. This is mentioned in the original instructions. I think this is where you went wrong, exiting the command window prematurely, leaving half-extracted packages and temp folders/files that are normally cleaned up automatically.
3. The resulting QTfiles64 folder created should contain all needed files and now you can move that folder, AND qaac64.exe, to the MusicBee "Codec" folder.
4. Finish the rest of the setup of MusicBee's File Converter dialogs as described in the original post.