Thank you for your reply. I'm not exactly sure how I fixed the second issue, but I did in fact resolve it. As far as the code goes, it was a dumb mistake on my part, not checking to see if the taxonIds variable had any child elements in it. So when a post didn't have one of my custom classifications set, it would throw the "Id cannot be an empty Guid" error. That makes perfect sense.
As far as the issue I had loading the content item itself to edit it's contents, I'm really not sure why that went away. I made sure every dll had copy to local set to true and redeployed my code, recycled the app pool in IIS, and it seemed to fix the issue. Will keep an eye out if it happens again. Thanks again Jen.