Upgrading AX R1 to AX 2012 R3

Hi,

I am upgrading from R1 to R3. I had followed all the steps from below link
technet.microsoft.com/…/jj733502.aspx
At the time of code upgrade check list I have not provided license information. I have done license information check list as mark as complete and then completed all the steps of code upgrade and data upgrade check list.

I can see that all the AX 2012 R1 modules are present while all AX 2012 R3 modules are not visible.So I reloaded the AX R1 license file. Now when I see AOT–>Menus–>Main Menu,

and compare mainmenu with sys layer i am able to see missing modules
but i am not able to import.
So what could be the cause of R3 modules not displaying. Is it license file issue or upgrade issue?

Thanks,
Surbhi