hi Olie
Route 1: Minato - Shinjuku - Kawaguchiko
1. I think it's better to take the Yamanote line from Hamamatsucho to Shinjuku. Oedo line from Daimon to Shinjuku conts 220yen and Yamanote line from Hamamatsucho to Shinjuku costs 200yen. Oedo line is faster but only 2-minute difference. It takes about 24 minutes by Yamanote line.
2. I think you must buy the free pass on the day of departure. The ticket counter opens at 8 am, so you can buy the ticket at 8 am and then take the bus around 8 am.
3. The ticket counter is lcoated on the 1st floor nearby the Odakyo line entrance gate. It's located at upstair of JR West Chuo Gate.
http://www.odakyu.jp/english/center/The hightway bus you should ride is Keio Highway bus at Shinjuku Highway bus tarminal. The Shinjuku Highway bus terminal is located at West Exit of Shinjuku Station nearby Yodobashi Camera.
https://www.google.co.jp/maps/place/%E6%96%B0%E5%AE%BF%E9%AB%98%E9%80%...Route 2: Kawaguchiko - Gotemba - Hakone
1. It takes 1 hour 10 minutes from Kawaguchiko sta. to Gotemba.Sta.
2. There is a bus to get Hakone From Gotemba Outlet Park, so you can go direcltythe Outlet by Fujikyuko bus from Kawaguchiko and then take a bus from Outlet to Hakone. How long you can stay in the Outlet depends on the timetable of the bus.
3. Here are the bus timetable for each bus terminal.
Shinjuku to Kawaguchiko (Keio Highway bus)
https://www.highwaybus.com/rs-web01-prd-rel/gp/info/timeTbl?lineGroupN...Kawaguchiko to Gotemba Outlet (Fujikyuko bus)
http://bus.fujikyu.co.jp/line/jikokuhyo/01.htmlGotemba Outlet to Hakoneyumoto(?)
http://www.hakone-tozanbus.co.jp/pdf/13223-002001.pdf4. Actually you use Hakonetozan bus around the Hakone area, not Odakyu highway bus. It's just a local bus so you cannnot keep your luggage in the bus.
Fujikyuko and Hakonetozan buses are normal local buses. I think there is a place to keep luggages, but you cannot keep your luggage in the bus when you stopped by, because the bus departures for the next bus stop immediately.
I think it's better to keep your luggages in a locker in Gora or Hakoneyumoto station.