I've been JBen for 7-8 months now, no problem so far except for the time where i asked the staff a question and I had forgotten to change the carrier name back...
About the foreign 3GS in japan, I'm pretty sure you're screwed. They don't offer our very good package plan to foreign iphones, as far as I know that is, and will make you pay A LOT for web access.
To give you an idea, my last bill read: internet access=840.000¥ (8400USD), internet access package plan discount=-840.000¥.
Broke a sweat first time I noticed.
I doubt it would be that bad, but you wont get the free access for 40$/month plan...
If you want to stay here for a year or two, i'd sign up for a contract, get a cheap/free 3G and swap the SIM card.
Either that or get stuck with a prepaid phone. I might be wrong though, if rules changed recently without my knowledge.
Anyone tethering in japan and still not in jail/debts?