Hi Yas. To get answers to some of your questions please ask your self what are you trying to archive with this model? How do you want to build it? If you want to assemble as per kit instructions, then follow the instruction provided. The kit supposed to give you all of the sizes for parts. Should you take a path to modify (bash) the kit, get your self a copy of the book:
Historic Ship Models by Wolfram Zu Monfeld (click the link). IMHO this is an indispensable allowance for novice shipbuilder in period ships. You would be surprised to find answers to most of your questions.