1 - Go for Manual if you are comfortable with it and want complete driving control. It's a pleasure to drive and more rugged/reliable than automatic. Go for automatic if you aren't comfortable/competent with manual, ladies (if any) at home are more comfortable with it or health issues prevent repeated movement for clutch engagement/disengagement.
2 - Leather options in all Honda cars sold here are useless. The leather sags within couple months and in summers, it is extremely hot and uncomfortable (for few minutes after you get into the car). Fabric rules. If you really want leather, go for aftermarket higher quality options.
3 - Don't opt for TW navigation unit. There is a thread here about the new system but Tracking World has lost my trust due to their shenanigans about their shitty product. Also, the system is very overpriced for what it offers and has crappy sound quality. Do check any available aftermarket options and consider using a dedicated tablet for navigation.
4 - Eurostars are tolerable but that is totally your own choice to use them depending on your budget and preferences.
5 - Your choice.
6 - Any of them works. Buy from whom ever is closest and will get to do periodic maintenance on your car.
Bear in mind that next model of Civic is due in Q3/Q4 next year.