Hey & thanks!
For cron, you need to adjust your cron job to point to the new scripts in the scripts
sub directory. The file to edit will be either /etc/cron.d/itflow
or by running crontab -l
For Stripe, you just need to ensure you have your Stripe integration keys & a payment account set. The client primary/finance contact can set up auto-pay via the portal. You can see the status of which clients have set up Stripe auto-pay at /admin_settings_online_payment_clients.php