I entered an email address that I guess was attached to my pay as you go plan, that I've stopped using, now the website says that I'm waiting for an email to join the accounts but I haven't received the email in over 24 hours
You'll need to contact Koodo to get it fixed. They will have to remove the old account information so the new one takes precedence. I suggest a Private Message to their Facebook page or a Dm to Twitter, rather than a phone call, as it will consume less of your time.
Looks like you already have an online account set up with us. It is with the hotmail email address and it seems it worked because just after you activated with us you validated the account and signed in. Now, there is another email address (an outlook one) on file and if you are trying to log in with is why you might be getting the message you received. Does this help?