Would different emails for iCloud explain why I've lost contacts & pics
Yes, if you haven't changed your primary email on your iCloud account from the "then" email address to the "new" email address, logging in with a different email means you are now probably using different Apple ID all together and are seeing the contacts and pictures –or lack of them– of this Apple ID.  

The proper way to change your Apple ID main email address is described here:


  
  Sign out of every Apple service and device that uses your Apple ID.
  Sign in to your Apple ID account page.
  In the Account section, click Edit. Under your Apple ID, click Change Email Address. You might be asked to answer one or more of your security questions.
  Enter the email address that you want to use as your Apple ID. A verification code will be sent to your new email address.
  Enter the verification code from the email into the fields provided and start using your updated Apple ID.
  Sign back in to all Apple services with your new Apple ID.
  After you change your Apple ID, you need to use your new sign-in information with all Apple services that you use.
  


Additionally, you're probably going to have trouble using the "new" email address now, given you cannot use the same email address for two Apple ID's. If you run into that problem, please ask another question (the solution probably involves adding a third email address to the "new" Apple ID, making it the primary email address, and deleting the "new" email address in order to make it available for use again). 
Sorry, there is no solution to the last part, apparently: Remove an email address from apple-ID