Most of your symptoms sound like candida overgrowth and agree that the stool test is unreliable potentially. Everyone has candida in their body and so its a tough test to determine whether you have it or not…because believe me, you’d be dead if you didn’t have candida in your body!
This diet is completely healthy so I would look at western foods as a problem and why you are here in the first place; gluten sensitivity and candida related health problems are becoming an epidemic and most people don’t tie it all together. Candida can cause diabetes, crohn’s disease, blood pressure problems, various types of cancer, etc.
The only thing that is similar to candida is parasites, and this could be a possibility as well. We all have parasites but at different levels. Testing for this often is inconclusive as well.
A good naturopath would mention that you need meat in order to be healthy, so I would consider this if possible. There likely is all sorts of deficiencies within the body because of not eating any, and I would look at it as a tool to get healthy. A good naturopath also would determine what organs, if any, are damaged currently and will help heal those specific organs with a treatment plan. For instance, the cold hands/feet could be from a slightly damaged thyroid but this hasn’t been tied together by your naturopath yet.
All I gotta say is to keep on your plan and try to alter your diet even more if possible. Nuts contain molds and feed candida; this can significantly set back your progress from my personal experience.