The beans cannot be pureed before canning, you’ll have to do that after opening the jar to serve. The reason for separating the solids is that each jar should only be filled half way with solids in order to be safely canned. You can certainly do this one jar at a time, I just find it easier to do them all at once so the solids are evenly distributed. Hope that helps!

Yes, you can use tomato sauce in it. Tomato puree is a little thicker and chunkier, but it really won’t make a difference.

If you chose to add fresh peppers you will need to reduce one of the other vegetables by the same weight to make it equivalent to the tested recipe this recipe is based on. However, according to the USDA you can freely add dried pepper flakes or dried spices to recipes without it affecting the safely of the tested recipe. To me, spicing it up with dehydrated peppers is just easier than worrying about the weight, which is why I replied the way I did.

@Angi Schneider, if you are canning the soup fresh peppers are fine.

You can safely add dried pepper flakes or other dehydrated peppers but not fresh peppers.

Yes, you can make both of those substitutions or even leave out the vinegar since it’s in the recipe for flavor, not safety, just know that the flavor of your soup will be a little different than the original recipe.