Is it reasonable to assume at the very best you could expect your base salary remaining give or take a bit each side depending on ones activities??
If you take the C class ticket option you don't pay for any tickets, so that removes one complication from the equation. If you choose to take the $2000 and use a ZED ticket, then you'll end up with extra in your bank account because no-one spends > $2000 on a ZED fare (if they did they deserve to lose money through sheer stupidity).
If you live in the hotel then the accommodation allowance will normally cover the costs over the course of a year. Sometimes you'll spend more in a month than the allowance but other times you won't. So, living in the hotel will mean you don't dip into the base salary. If you live by yourself in an apartment then you'll be using some of your own money to cover the cost. Sharing will probably work out similar to the hotel.
Food and drink are a variable feast (do you like what I did there) but you've basically got $1000 to spend during the 20-odd days that you're 'on the job'. Japan is expensive but some of the places we go are pretty cheap. I think it is fair to say that you can get by on the per diem element without encroaching on the basic pay.
With the recent tax hikes in Japan it definitely costs more to sleep and eat than it used to and, so far, none of the contract companies has bothered to get their finger out and press AJX for an increase to the allowances or per diem. I believe we are right on the limit of the allowances covering what they are meant to but any further price rises, particularly in Japan, will mean dipping into the basic salary, which is clearly unacceptable and will have to be actioned by the contract companies whether they like it or not.
So, in answer to your question; living in the hotel I think it is reasonable to assume you can bank on banking your base pay. Sitting down the back of an aircraft on a ZED ticket to commute home you can guarantee banking a bit more.