OK, I got it working for real.

It's
mostly drag and drop over FTP. The only obstacles were my own stupidity and some counter-intuitive interface choices in the emulator. If I could write a guide to my past self it would go something like this:
1 Make sure everything copies correctly over FTP. It's not as simple as USB.
2) The games need to load. So if you start a game and the screen is blank while music plays, it's not broken, it's just loading. It just doesn't tell you that.
3) The interface for loading floppies into the disk drives/hard drive within the emulator is really counter intuitive. It goes something like this:
While in the game list menu:
A button = loads the selected floppy and boots it up in the x68000 emulator
X button = goes to the menu where you can choose what to load in your two floppy drives (A and B) / hard drive
While in the menu where you can choose what to load in your floppy drives / hard drive:
A button = takes you to the game list menu so you can choose which floppy to load in the drive
B button = launches the X68000 emulator with the floppy drives loaded with whatever you chose
4) Minor Japanese literacy is needed in some cases. If you can't read Japanese you'll need a guide or one of those smartphone apps that translates kanji through your camera or something. For example when you start Akumajou Dracula it asks, "Which sound module do you want to use?" (FM, external midi, etc). "Hard drive corrupted" and "Incorrect disk not inserted! Please insert correct disk." messages are in Japanese too.