Starch is the problem and not carbs in my opinion. You need carbs to survive.
I would place the quinoa and brown rice products in the same category; high starch food items high on the glycemic index. I would save both of these for stage 3, which is basically when you become symptom free and are long over die off. I have been on the diet for close to 2 years and didn’t start to eat rice products until 6-9 months into the diet. And if you do eat them, eat them very sparingly…no more than once a week. Rice and quinoa can also be problematic to digest; I personally couldn’t digest either of them very well for a long time. Fermenting foods in the gut needs to be avoided at all costs.
Black, red, and wild rice are better alternatives to brown rice because they have greater nutritional properties and you likely have not had them in your lifetime.
If you soak and/or roast the nuts, this will remove most of the molds. I wouldn’t introduce these until stage 2 or when you are over die-off and feel pretty good.
Chia seeds, pumpkin, flax, and summer squash are the safest food items you listed. Chia seeds and flax will contain molds but at lower levels when compared to nuts. Cooking these items typically will kill off the mold. Summer squash is a bit more unhealthy than pumpkin which is highly anti-inflammatory and has a number of benefits. I have a post about the benefits of pumpkin somewhere on the forum. It will help heal leaky gut and remove the toxins.
If you are planning on consuming pasta with tomato sauce; keep in mind that tomatoes contain high levels of sugar when concentrated in something like a sauce. A cup might contain 20g of sugar. Tomato sauce should be a stage 3 item in my opinion. It’s also a fruit and not a vegetable. Nightshades can be problematic for many on the diet.
I would eyeball servings of beans and look at the bean family. They are high in starch but have a number of benefits and are generally less problematic than a number of other foods.