Mr. V did provide 2 links where one could discover how to.
But ... basics below ...
Site course backup defaults is set to include users and data - everything is in a course backup for the course.
Your Windows 3.3 does have admin/cli/backup.php which could be looped through a text file of course ids that belong to a category. Example site has a social studies (ss) category ID 3. Query of DB that dumps only the course ID numbers from category ID for ss to a text file. That text file is used in a looping batch file to run admin/cli/backup.php with parameters to save backups to a destination directory for all ss courses (course ids may not be sequential)
On the new server, all those ss course backups are uploaded to a similar directory structure and temp in admin/cli/ of that servers code (shorter command line and moosh commands must be called from within code directory).
On new server. Create a category for ss. Know it's course ID number..
moosh is installed on new server. From that ss directory that contains all the ss course backups use the moosh command to restore each course backup contained therein to the ss category of the site.
For each category on old site, wash, rinse, repeat.
Potential catch 22's ...
admin user on old site was enrolled in a course.
addon plugins used in the 3.3 doesn't exist in the 4 or the plugin doesn't have a 4 version.
Themes are plugins ... set 4 site to force the use of boost. After you get a catetory of courses restored, might query the DB for courses in that category to see what theme each course is expecting ... then correct if any are trying to use a theme not installed.
Once did a site like above ... 4000+ courses ... took hours without a break as 'customer' needed it yesterday! Doable but you'll be brain dead when finished! 
'SoS', Ken
