Well I finally managed to get it to work but not without hacking the crap out of the boot.exe file.
Ill write down all the steps before i forget.
I created a brand new wine prefix (wine staging 3.8-i386) for the 10th time, with a new install of the game, new launcher, and followed the steps above. Note that in 32bit windows jpDLL.reg needs to be modified. WOW6432NODE needs to be removed from the paths and any path with " Program Files (x86) " be changed to "Program Files ".
End result of the reg file will look like this for windows 32bit. If using windows 64bit there is no need to do this.
Windows Registry Editor Version 5.00
To deal with Ashita\ffxi-bootmod\boot.exe
All I did was open boot.exe in a hex editor and went to the strings section. The section that starts at the offset 032809 bytes.
Replaced any instances of "PlayNasomiUS" and "PlayNasomiEU" with "PlayNasomi", replaced any instance of "SquareEnix" with "Square".
I dont know if this has any effect but i also added new keys in the registry since it was referencing it in the boot.exe file:
In the "Settings" key I added a DWORD with name "Language" with value 0.
Then I started the game with "boot.exe --lang JP" and was miraculously able to boot in Japanese.
The strange thing is in the registry PlayNasomiUS still gets made, and the game uses the graphics and pad config from there.