Is there a way to source what is changing a skill
 

Something is giving this character Proficiency to Perception. I have tried to find the common source, and cannot find it.

Is there a way to audit the character to find out what is giving this bonus?

Without know your race, class, background, archetype is impossible to know or advist you

I don't think you can track it via the debug options. proficiency is granted via a tag assigned to the hero or an object attached (background, weapon, etc.) and there are literally dozens of tags per object even if you narrow down which tag you're looking for it could potentially return too many results. .

You would need to post the .por up here for someone to download. If you're using custom files of your own, we probably can't help much.

I would spend time adding/removing things that are likely culprits.

A magic item is also highly likely to have a Perception script attached if you've already changed the background out or changed the subclass for a quick check.