Ive gotten rare guns to show up in the armory on quick matches, but they wont appear in campaign or Coop. Is there anyway to get them to appear in online Coop and Campaign?

I think you could find the answer into Mods section since I've read something similar to your question.
Well, Pasi will advice you better.

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Take a look at weapons\invasion_all_weapons.xml, many weapons have additional changes there that are applied when playing campaign.

If you're creating an overlay mod for this, rather than editing vanilla files directly, you also need to have overlay_config.xml in your overlay folder to get it to show in the custom campaign list. The contents would be