357k for 16 days is WAAAAAAAAAAAAY too much and MORE THAN ENOUGH to spend without thinking too much if you are not buying a lot of branded goods (not talking about cheap stuff like Gucci, i mean stuff like Hermes...).

I took 90k there for 10 days just for eating, light transport (JR pass not included) e.g. taxi, bus and subway, entrance fees (Disney and temples), and some light shopping and still got some money left when return.  FYI, eating there is not as expensive as you think, previously I thought for lunch is around 1000 yen, for dinner around 2000 yen but that's considered an expensive meal already.  you can easily find 800-900 yen for a very satisfying lunch or dinner.  from my experience, if you see a stall / small shop that has people standing and eating (no stools, no proper tables, no chairs) then it's a good place to eat.  if you see people (locals) lining up and have time, go do it, it's probably great.  And these kind of places are often VERY CHEAP, ranging from 600 - 900 yen with large portions of a meal, and 99% of the time they taste excellent.  The very best ramen I've ever had are either lining up for 20 minutes or need to eat standing up.

For Tsujiki Market, if u r planning to have a full meal of 1st grade sushi, prepare 10k yen, but if u plan to have your raw fish at local stalls (at back alleys) and also have misc food (like char grilled scallops, salmon row, uni) at different stalls, u don't even need 6k.  i personally like the 2nd option, u can't imagine the choices they offer there!  start at 9am and eat until noon.
for Disney u don't need to buy it online if you go there during the weekdays.  Just start your journey earlier, arrive at around 8.30am and u'll be fine.

you can get the ticket at shinjuku

my advice to u for the data is to just get a sim card or a LTE mifi in japan, it will be a lot less (for mifi) and it will be a lot more reliable and so much faster (data speed) than digi.  make sure u book it early, they tend to sell out pretty fast.  for GPS, just use google map, it's quite reliable although sometimes it can't find your exact position in subway stations.  but it's ok, because u only need to know what station u r in to find what train to take next.  if in doubt, ask people.  if u have JR pass, don't forget to utilize it fully if u are taking JR line trains, u don't need to buy ticket or use the IC card, just show the JR pass to the attendant at the gate and they will let u through.

i didn't see your schedule before posting, so i'm not aware that u are going for onsen, the spending there will be higher than big cities like Tokyo...

you can't plan your train schedule exactly, u will have to modify your schedule accordingly.  my schedule changed a lot when reached japan, 50% of the places I planned to visit i didn't manage to go because i was traveling with a bunch of girls, but if u are traveling alone then it will be a lot easier.  and yes, your legs will suffer, if u do not often exercise, u will suffer more.  just get some stickers for muscle pain in the shopping center in japan, remember, expensive is NOT often good in this category, buy those with middle prices, they will help your get through.  try 1 box first, if it's no good, change brand until u get one that works.  without them, i can't survive my 10 days trip.

You can skip the capsule hotel and sleep at Haneda Airport, the International Terminal, of course. Its safe. I did it twice. Just find a spot away from the escalator. My MiFi was with Wireless Japan. You can Google for it. They will send to your hotel.

Which brings me to a query; can we sleep at Narita Airport? Or KIX?

Looking at other people itineraries makes me excited as well. Haha.

actually it doesn't cost this much (14850 yen) for the mifi, u can see with this website:

http://www.globaladvancedcomm.com/pocketwifi.html

it's only 7950 yen for 15 days (75mbps LTE) and the delivery is free in Japan, just pick it up at the airport

for the muscle pain, i have to find my photos and see whether got capture a picture of it (got more than 2000 pics so need a bit of time)

I bought my ticket online. Did not encounter any problem paying with my debit card. Just need to print out the ticket on a4 paper to bring there.