I’m arriving at 9pm on day 1, will this be a problem?
Not at all. Nothing is scheduled on day 1 apart from the group getting together in the evening at the hostel near Ueno, so if you land late you will simply meet everyone the next morning. Let your leader know your arrival time.
Trains from Narita and Haneda into the city stop running around midnight, so if your flight is delayed, a taxi is the fallback. Your pre-departure information explains the options.
