Custom Icon Design Issues

So one day I decided to combine the Sifr icons with Tango because I didn’t like how the launcher of the program looked all black and white with the icons so I decided to merge both Sifr and Tango icon packs to create what I wanted and I noticed three things.

  1. I would no longer get automatic updates
  1. I would have to recreate this custom icon theme every time I installed an update
  1. Not all icons are showing up and Breeze replaces some random icons for no reason.

Is there any way I could force all Sifr icons to be present without affecting the Tango icons I want and to make sure that this custom icon design pack is always present in updates? I tried to change the name of the icon pack but i ran into some very weird issues so I had to just overwrite the Sifr icon pack.

Here are some screenshots of my issues and the current designs:

Splash screen:
Document page:
Icon Issues: