I would remove all the products and categories at least and reset the autoincrement values in the tables. Your product id values are massive which shows that there has been a lot of stuff added and deleted from the tables. It would be easier for you to start again with a fresh install from scratch.
Product importing is and has always been a complete nightmare - which is why 3rd-party developers have made money selling product import and store manager modules. For years.
You don't need to worry about the nright and nleft fields. Those are used internally. Editing a category causes the tree to be rebuilt which is why they suddenly appear when you do that.
With import files you need to be very careful that things like category names match exactly with no spaces before or after.