I hate to also say this, but that shop isn't going to make things right. They are cutting corners and avoiding working on your 4Runner. I also don't know if all the interactions have been civil on both sides. You mentioned the owner yelled at you for not calling ahead, you might be on their 'bad list' and you are never going to get good service there again as they know they can make more money working on other people's cars that are not warranty services. They way I see things, you have a few options:
1. Keep bugging them to fix your 4Runner. This may never have resolution as they will eventually just decline to fix it. You might already be at that point.
2. Pay another shop to fix it. This will be expensive considering you now have a transmission issue.
3. Sell the 4Runner. Yes, I really mean sell it. The nightmare will be over.
Contrary to how it may seem, I do have shops work on my 4Runner for more complex jobs and when I do it's always the dealership. I know if there's issues they will make it right, every time. There is a price for customer service and taking pride in their work, as I've never had a job done wrong at a dealership for any of my cars. Before then I went to a private shop with good prices to work on my 91 Toyota as I was also learning to fix simpler jobs myself. They changed ownership and replaced most of the staff. On one time after an oil change they told me I was due for a timing belt change. They had just done that same job 1 year and 5,000 miles ago at their very own shop. I never went back.