Hello again! wow lucky you. I've been to Japan and its fantastic! When my little sister was 3 months old we travelled around the world with her and its so much easier than people think.

A few tips:

I don't know what the weather will be like but it was snowing when I went so lots of layers is good for Alistair
Also as you know its very crowded so put him in a frontpack when possible.

He will need to suck a dummy on take off and just before landing for his ears if he doesn't take a dummy see if you're allowed to give him some water or milk at this time.

He will be put in a basinnette in front of your seat and you can change him in there. Flight attendents are usually wonderful with children and they'll probably try to score a cuddle.

Take a few of his favourite toys, something musical and teething toys.

I thought babies did get a baggage allowance but it may have changed. If no baggage allowance I wouldn't take a stroller, just buy a cheap one there, unless you can find a compact light weight one maybe.

If you still have samples from your bounty bags take those with you. Take a pack of change mats and nappy disposal bags. Take some baby panadol, vix baby balsam, moisturiser and anything else that he might need for teething, reflux, wind etc.. Take enough nappies for 2 das and buy the rest there.

don't worry about stuffing up his routine, kids handle jet lag much better than adults. I bet after/during this flight you'll feel very confident to take him anywhere even on your own.