I have an older iphone and the icloud email is my work email and the iTunes and App Store has my home email. I bought a new phone today but they were not able to transfer files, apps or photos to my new phone.

You will not get access to any of the iCloud (work email) data unless you sign into that account, preferably on a laptop, and export the data to the hard drive, then sign into icloud with the new (home) address and copy from the hard drive to the new iCloud account.

You will need a device trusted by the work iCloud ID, like the old phone, to receive 2 factor auth codes.

It isn't an easy process and uou may need professional help. The hardest job will be manually copying passwords if you used Keychain.

Which email address did you use to activate the new phone?