Wife

My wife and I each have iPhone 4S and my son had an iPad 2. All three devices shared content from the same iTunes account, but my wife and I each used separate e-mail accounts/iTunes accounts for the Cloud because we ran into issues with her receiving my texts when all were under the same account. We just replaced the iPad (it died) with a new iPad Mini, and when I was installing it, I chose the "Replace with iTunes" function to basically take everything from the old iPad and put it on the new one. All seemed well. However, I received an alert this morning that my wife's phone was now using my cell number for iMessage and Facetime. Immediately after, I texted her and asked if she was having issues. She tried to text me back and it responded to my phone as well as hers. Now, any iMessage texts that people send to my number go to her phone; plus, any iMessage texts that I send are received by others as being sent by my e-mail account, not my phone number. I went into Settings and turned everything off for the Cloud, and my wife did the same for her phone and the iPad, but no change. Anyone have any suggestions? Thank you...