Hi,
Do it this way.
On the Mac Shut down the Messages app
On the iPhone go to Settings > Messages.
Remove the Apple ID.
Place the iPhone in Airplane mode for 5 mins (this breaks with the server)
On restarting the iPhone in normal mode go to Settings > Messages and check the app is active, that the iPhone Number is listed and that it is greyed out but ticked as Active.
Re-add the Apple ID.
The break with the server and re-adding the Apple ID will cause the iMessages server to re-link them.
Now restart the app on the Mac.
You should one or two pop ups saying the iPhone is using the Apple ID and the iPhone number.
Accept the pop up(s).
Accepting the pop ups adds the iPhone number to the list in Messages > Preferences > Accounts > iMessages account for the Receive At and the Send From drop down.
9:13 pm Wednesday; November 6, 2013
iMac 2.5Ghz 5i 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad