Support will not be provided for forked code. Honestly, it sounds like you've overcomplicated the menu on your site.
If I understand your requirements, you need to have a different menu on different pages of your site. If that's the case, you can easily build your own menu using the list module or even just html content. You could then build as many of these "menus" as you would like, one module instance for each menu, and using the "Global Content" feature, place those menus on the appropriate pages. To place the menus in the header of your site, you'll need to move AltContent1 to the header and then place the menu module instances in the "Top Content" pane.
The solution I outlined above will not fork the code and you could have it finished in a matter of minutes.