Before you do anything, make a backup of the iPad to a computer if you can.
In my experience @books453 is right and iOS asks what you want to do with photos and other iCloud data when you sign out: remove them from the device or leave them there. They should then be able to be added to a new iCloud account when you sign in with it. However, I don't know whether this applies to data stored in apps and games, such as game scores.
When you say I changed his email address for iCloud via my laptop when I set up his phone, it sounds like you actually created a new iCloud account for him. If you had in fact changed the email address associated with his iCloud account then I don't think Apple would still be sending confirmation emails to the old email address, as you say many other people have already told you (sorry to repeat it!). To verify whether the new email address is attached to his old iCloud account, log in to http://icloud.com/ with the new email address and see whether the photos and other data from the iPad are are available there - if they are, I would be confident that the replacement of the email address has worked and therefore it should be safe to sign out of the old address and sign in to the new address.
If this was my device and data, I would make an appointment with the Genius Bar at a time when the Apple store won't be busy and ask them to walk through the process with me. Your son's new iPhone should entitle him to at least one session of personal setup assistance and technical support. And don't accept what the first Genius tells you if it's not what you want - get a second opinion, as this is a tricky case that not all staff may be familiar with.