I built CEM CLI for this purpose 
cPanel to EE migration. The new version even supports subdomain migration.
Resources
Labs: https://labs.ahmadawais.com/cem-cli/
Blog Post: https://ahmadawais.com/introducing-cem-cli-move-cpanel-easyengine-ease/
GitHub: https://github.com/ahmadawais/cPanel-EasyEngine-Migrate-CLI
EasyEngine Blog: https://easyengine.io/blog/cem-cli-cpanel-migration/