First you should not modify any mojoPortal source code, so don't think in terms of changing things in .cs files.
The way the google analytics scripts work is that at the top of the page an array is declared and you push any supported google analytics things into the array as in the sample code I posted before. Then at the bottom of the page the google script will process all of the items in that array. So adding a custom script that pushes custom variables into the array should not cause any problem. If you view the source of the rendered page you should be able to see what the google anlytics scripts are doing.
Generally I would put the script in the layout.master file of the skin but below the top google analytics control.
However I don't know how you would get the needed data from there (you could detect the user from server side code but again it is against the rules to push the user email or any other identifier into google analytics), it would be best to implement a custom usercontrol and embed that in layout.master then from code behind you can do any server side logic to determine what your script should do.
Doing these things does require knowledge of asp.net