You should include your dual time in your total flying experience. Are you sure there is no field on the form to enter dual or PUT time, as I seem to recall there was (albeit some time ago now)? Clearly they are the same thing.
If there is no dual/PUT column then I would put it in the P2 field. The main thing is not to claim for PIC when you weren't and this, in my view, would be the best way of doing it.
As for cross country, until recently there were very few logbooks which had a X/C column and it's certainly more of a judgement call than entirely specific. I believe anywhere outside 7 miles or so from the airfield qualifies as cross country, so my advice is to look through your logbooks (especially early days) and subtract the circuit details from your totals and what remains is cross country and hopefully that will exceed 100 PIC....or it's no ATPL for you
There is no requirement to have it logged separately (until you get your JCAB logbook) and the Japanese do understand that different authorities do things differently. Just make sure you are able to show how you arrived at your figure......i.e. you've taken out all your 'local' flying.