As the guy from the japanese consulate told me to expect my visa 4 days after application I was getting somewhat nervous, as it's been already well over 2 weeks. But yesterday I finally received my passport back, with the visa stamped in.
That was the last hurdle out of the way...
To wrap up some other things: I booked my flight with swiss (as they are the only ones to offer direct flights from Zurich). Furthermore I got the OK on my flat. I'll be staying at "Plume IS".