IOS – Japanese kana layout on iPad screen keyboard

You can use the app Ukelele to fairly easily make a custom layout that puts the punctuation where you want it.

http://scripts.sil.org/ukelele

After making and installing a custom layout, you should be able to select it in the Kotoeri Preferences.

You set the Latin keyboard layout for Japanese input in the Kotoeri Preferences. For Chinese, the IM normally uses the last Latin keyboard layout that you have used.

Settings you make in the system preferences/language & text/language or formats tab are irrelevant for the keyboard layout. Only the input sources tab affects that (and Kotoeri preferences when that is chosen as an input source).