I had a great time in Japan (aside from the heat and humidity), but at what cost? Japan is pretty pricey, and while I avoided splurging on much, I didn't try very hard to save money either. These numbers might help someone thinking about visiting Japan.
Before the trip even began, I booked the flight, got the JR pass, and booked most of the hotels.
Flight: $1,228
JR pass: $356
Prepaid hotels: $244
Aside from the capsule hotel, which was about $36, hotels I stayed at ranged from $50 to $80 per night. I think this is about the low end of what's reasonable aside from hostels or sketchier/less convenient locations. One night was free because I crashed at V's.
Over the course of the trip, I withdrew ¥80,000 for a burn rate of about ¥10,000 per day (excluding the last day). The last day was the cheapest at ¥794 because we didn't do anything touristy, we were just getting back to the airport. The most expensive day was the day I figured out how to efficiently buy manga; Friday cost me ¥13,279.
Hotels: ¥13,700
Trains/buses/taxis: ¥11,620
Obviously, depends on how much you travel. We took a bunch of not strictly necessary taxis, which added up to about ¥4,000.
Sightseeing entrance fees: ¥4,075
Obviously, this depends a lot on where you go. Most places were about ¥500.
Meals: ¥17,964
This is a little more than what I actually ate, I paid for other people's meals twice as thanks. There was one splurge breakfast at the fish market for ¥3,900.
Snacks: ¥5,234
There's some overlap between this group and meals; I would consider snacks more optional. Then again, if you skip all the snacks, you'd probably eat more for the meals. This is a bit high because it mistakenly counts some gifts, which I got at the same time as some snacks.
Souvenirs: ¥5,401
Obviously depends on how much you get. I only got a few gifts and some cheap anime trinkets.
Arcade: ¥3,000
This was for two people; I treated V as (partial) thanks for the place to sleep.
Manga: ¥16,435
You're probably not buying this much manga.
Miscellaneous: ¥1,205
Unspent: ¥1,366
Travel tip of the day: If there had been an extra hour or two for shopping at the end of the trip, I would have avoided ending up with unspent money. Managing money would have been less worrisome towards the end because I'm sure I would've found something to spend it on.
At an exchange rate of approximately ¥80 = $1, the trip cost about $2,800. Cutting out the manga, arcade, and taxis brings it down to about $2,500.
Of what I paid, about 43% was for airfare, 18% was for getting around, 15% was for lodging, 10% was for food, 7% was for manga, 3% was for doing stuff, and 2% was for souvenirs.