hy, i have experience with citizens, but not with b axis .... i googled it : yes, looks nice
i have good manuals for citizen, but not with b axis ... look inside yours, maybe there is something
i would measure it like a normal tool, and try to use it without rotating ( maybe in mdi, or by creating a small program ), at least to have a clue if offseting works ok... after that, i would activate the b axis, and check again
it may be possible that B axis has it's own wcs, in respect to the pivot point ... ask for a cutting code from your dealer / kindly
ps : is not a must to use a lh tool for cutting, you may setup up the cut-off / facing however you like ... it may be possible that during cut-off you have somehow a shifted coordinate; do you have experience with normal citizen, without b axis ?