Finally figured it out. Default layout for the HHKB P2 was GB which thinking now makes sense. Changed the /etc/default/keyboard to US from GB and then no variant (was extd) then removed the lvl3 options and made the win keys control keys with altwin:ctrl_win.
switches on the board 011000
XKBMODEL="hhk"
XKBLAYOUT="us"
XKBVARIANT=""
XKBOPTIONS="altwin:ctrl_win"
All keys work exactly as printed (except for my change to the win keys) and no issues.