I just went ahead and deactivated my iMessage to see if i could replicate what you were at.
From my testing around with activating my phone number for iMessage AND Facetime, I found that you need to 1. Turn off both iMessage and facetime.
2. Go into Facetime settings and select use Apple ID for facetime
3. From there log in and select ONLY your iCloud email to recieve text messages at (If its not there select ONLY the email you originally made your apple ID with) [You can change it after activation so dont worry]
4. Once facetime is activated go to iMessage and turn it on, Log in using the iCloud email as your Apple ID (Or the original Email you made your Apple ID with)
5. Again select only the same email that you used to log in. You should be activated with your email and it should say "waiting for activation" under the imessage on and off switch
6. Go to the PHONE settings pane, and change your number from +1 (123) 456-7890 (the numbers are place holders for your phone numbers digits) to (123) 456-7890. And tap Save
7. Your settings app may crash or it may go back, to the previous screen.
8. From there go back into iMessage and see if your Phone number is now there.
9. If not go to the app switcher and quit the settings app by holding down and pressing the minus button.
10. Re-open settings and go back to phone, and re-add the +1 before your number and go back to iMessage and wait for activation.
I did this 3 times and it worked all 3 times so please follow each step carefully!
NOTE: +1 is the United state country code, make sure you know your country code for this. As far as I know only United States users have the iMessage activation issue.
Good Luck and let me know how it turns out!