After a tense moment with Japanese immigration, I made it to Tokyo.
My form says I'm visiting Tokyo for tourism. The clerk asked me about work and seemed to think I was an indigent vagrant. I told him I was taking three months vacation (mostly true) and he raised an eyebrow. After some page flipping, he stamped me through, and I vaguely sensed his sadness as he waved on the next in a long line of foreign visitors.
If you're going to stay in Japan this long (three months), make sure you book your return flight and have your confirmation ready to show - they do ask. I am now legally required to leave this country no later than 11.8.