Hello,
Hope you doing well. My self Bharat Khunti and I have 4+ years working experience on SharePoint, office365, C#, JavaScript, jQuery, csom, jsom, PowerShell, Power BI etc.
So I can create PowerShell scripts to read all users from office 365 domain and get contact for each user as csv file.
I got you 2nd point that you want to generate one general file that has total number of contact for each users.
But can you provide more details about you 3rd point. what I understand was you want to make some changes on csv file for any user and import that file and update contact as per file.
I am looking forward to work with you
thanks
Bharat Khunti