Flying to Tokyo and back in economy class isn't anything to worry about as such. That's how the vast majority of people travel between Europe and Australia, let alone a much shorter distance between Europe and Tokyo.
Don't get weird ideas from this forum that economy class is something punishing - it isn't, as long as you do not have any extenuating circumstances such as being exceptionally tall, injuries, illnesses etc.
Contrary to what was earlier said, £2,000 for 2 persons from Glasgow to Japan and back in economy class isn't particularly expensive for the destination, depending on when you are looking at doing it, although I think you may be able to get the fares down a little, to perhaps £750 each, if you pick an off-season date, even on BA. If you take other carriers, you may be able to get it for a fair bit less.
Warning: If you are going for rugby or thinking of the Olympics, look at the hotel costs at the destination before committing to it...