Thanks for the reply!
I haven't really modified the brake light circuit at all from the stock harness, so I'm not sure how it could be wrong, but like I said I'm not good with wiring.
If you see a problem with my harness, I'd be happy to see any corrections. I'm up to at least try anything that might fix the issues.
Here's the stock harness diagram that I am working from, I tried to modify it as little as possible to avoid issues like this.
I have some time tomorrow. I'm going to go through and check my grounds to see if that clears things up, too