Yes, I did follow the steps written into this link, I am pasting these steps here for your reference and also please have a look into my comments on each step. I also mentioned the steps which I followed and in what sequence.
You must install one of the following updates if you plan to run Enterprise Portal on either Microsoft SharePoint Foundation 2013 or Microsoft SharePoint Server 2013. Choose an update that matches the SharePoint version on which you plan to deploy Enterprise Portal.
Update for Microsoft SharePoint Enterprise Server 2013 (KB2767999)
Update for Microsoft SharePoint Foundation 2013 (KB2768000)
[Faisal] March and June updates for sharepoint server have been installed and later I also installed the SP1 for sharepoint server 2013.
After you install an update, you must run the SharePoint 2013 Products Configuration wizard.
[Faisal] I ran this wizard before installing any updates, I ran this wizard right after the installation of sharepoint server 2013. I don’t know will it impact on the installation process of Enterprise portal or not. If Yes, then what impact this has been done on the installation and where It has done changes which would create issues in Enterprise Portal installation.
Download and install the Microsoft Dynamics AX 2012 R2 setup hotfix (KB2830441).
[Faisal] I have installed CU7 of Dynamics AX 2012 R2 which was released after this hotfix and includes this hotfix too. Do I really need to install this hotfix after CU7?
Download and install the Microsoft Dynamics AX 2012 R2 claims-mode authentication hotfix (KB2824690).
[Faisal] I have installed CU7 of Dynamics AX 2012 R2 which was released after this hotfix and includes this hotfix too. Do I really need to install this hotfix after CU7?
Reboot the server and then install Enterprise Portal. For more information about how to install Enterprise Portal or Enterprise Search, see Install Enterprise Portaland Install Microsoft Dynamics AX Enterprise Search.
I also want to add one more thing here; I have followed this architecture for the Dynamics AX installation.
Server 1: Dynamics AX Application server Dynamics AX 2012 R2 with CU7 has been installed
Server 2: SQL Database server Dynamics AX 2012 R2 reporting extensions and analysis services has been installed through Dynamics AX setup wizard. All the reports have been deployed and are running fine.
Server 3: Sharepoint server 2013 I have been trying to install following components of Dynamics AX on this server; Enterprise Portal and .Net Business Connector. When I run the pre-requisites wizard it gives me the error message which I mentioned in this support question. I know the Dynamics AX wizard only validates all pre-requisites on the current (local) machine where this wizard is being running. How this wizard will know that required updates or CU has been installed on application server as required in step 3 and 4 in your suggested Microsoft link.