Working visas, student visas, tourist visas, working holiday visas, marriage visas, child and spouse visas, re-entry permits, alien registration, gaijin cards, zairyu cards, permanent residency and all other immigration concerns.
A Y.K setup is a real pain in the ass. It'll cost you a bunch of cash and you'll have to get a VISA in order to stick around. I'd suggest picking up the Tokyo Classifieds and finding a lawyer to handle the paperwork. You can also go to JETRO...but those people are pinheads. I found a lawyer through JETRO though, and he's setting me up at the moment. It's taken quite a while and I'm still not certain if everything (including VISA) is going to pan out like I hoped.
It wouldn't be a bad idea to gather info at JETRO...but you're on your own when it comes time to make the moves.
PM me and I'll get into further detail if you would like. I can provide some contact names including my lawyer's who isn't bad (a little wierd) but not bad.