See my answers to your questions below.
1) Everyone Group has to be migrated from BO 3.1 or not? - No
2) Administrators Group has to be migrated from BO 3.1 or not? - No
3) Administrator User has to be migrated from BO 3.1 or not? - Np
4) Shall I have to select: Applications CMC, (ii) Designer, (iii) Infoview (iv) Webi etc.? - No
What options to select:
Export selected objects and their dependencies
(ii) Export selected objects
(iii) Export objects only if they are depended on
Select first option
5) While migrating Groups, which option to select:
Export this group, its subgroups, their users and their users dependencies.
(ii) Export this group, its subgroups and their users
iii) Export this group, its subgroups and their users only if they are depended on
Select 1 st option. But make sure 3rd party plugins like LDAP or AD configured first before moving the users and groups.
6) While migrating Folders, which option to select:
Export selected objects and their dependencies
(ii) Export selected objects
(iii) Export objects only if they are depended on
Select 1st option. This is not necessary, if you select the objects and their dependecies, folders structure also included