It's actually a more simple fix than I thought. I was able to fix this tonight using Apple's help after trying for weeks to figure this out.
All you need to do to remove a phone number you no longer have access to is to log out of Apple ID in both your iMessage and FaceTime & then change your password. Simple fix!
Go here and click on "how to unlink a phone number"
http://support.apple.com/kb/HT5538
Note: If you no longer have access to the iPhone that is using the number you want to remove, reset your Apple ID password.