If you want to stay longer then “monthly mansions” i.e. rented apartments, can be good, but if it’s anything less than 30 days then hotels are usually cheaper.

Travel around inside Japan is probably the most expensive.  Sometimes I can fly internationally cheaper than flying between the Japanese islands.  If you can get a Japan rail pass, then it’s probably worth it.  Or just stick in one or two locations.   I love working in Coffee Shops in Japan, Starbucks and things really have the old “we could run an internet startup from here” feel, unlike places in Europe!   People are also very friendly which is cool.