Some questions labels are not sent in email notifications

Also when the email is coming through - some question labels are not sending through, how do I ensure the form has the question in the email form once submitted. 

To ensure that the fields in your form updates the fields in your email notification, I would suggest that you create new notification https://www.jotform.com/help/25-Setting-up-Email-Notifications.

If email body is customized or modified, when you update the labels or add some fields in your builder it won't update the email body as it thinks that you have a customized notification. If the body is in default, all changes should reflect notification's email body.