You're always welcome!:)
1. No, unfortunately. I also wish that we could have 24 hrs transportation.
The trains operates around 1 am, and the buses are the same.
Some buses operates night-rides with extra fee around Tokyo area, but the only and easiest option would be taxi.
2. According to the website, the ticket doesn't accept reserved seat. But you'll be able to sit together if the bus you will take has enough vacancy to sit together. I recommend you to check-in as early as possible, and worth to ask at the office to arrange your seats will be close.
3. The highway bus's fee for round trip is 3,500 yen. There seem no discount.
But if you already get FujiQ Pack ticket, you don't need any extra fee for way back, included!
You need to select the date and time you will board, to FujiQ AND to Shinjuku ( or the place you'll get back) both in the same time when you make booking online.
Hope this can be your help!
Don't hesitate for more questions!