Alt + shift cycles between installed keyboards, so if you uninstalled the local one by mistake is not going to help. Also, Windows uses the default keyboard at startup, and I am not sure if alt + shift works there (I know you can do it when logging in after the screensaver pops up or after locking the session).
Go to the language configuration in the control panel and check what languages you have currently installed. If the layout you want does not appear on the list, you can simply click on 'add' and select it from the list. Then make it the default layout and then it should work at startup.
If you can't login you may want to look at an actual Japanese layout, if I recall correctly even those have a system to type Latin characters. Here is a wikipedia link explaining how Japanese input works: