Regardless of how it came to be, you still have an unanswered question. I would say you have three options for fixing the harness.
First option: Dealership. Obviously, this will be the most expensive, but it will get you a brand new harness.
Second option: Junk yard. You can find some pretty good condition items in junk yards, and pay very little for them. Now with that small invention known as the internet, you can search databases nationwide to find just what you need (try
www.car-part.com).
Third option: You can look in the wiring diagrams, and determine the differences between the two (for the automatic & manual), and make what ever changes you need to make to existing wiring. If needed, add wires and run them to the switch etc according to the wiring diagram. You can order pins & plugs from dealerships.
Also, when I mention dealerships, I honestly wouldn't use my local dealership. I would go online to 1sttoyota, & others, simply because their prices will be lower than walking in to your local dealership.
I'm all for supporting my local businesses, but when it comes to getting ripped off, I draw the line. I'd much rather go to a 'mom & pop' store than Walmart anyday. But money doesn't grow on trees, and I'm not too keen on just giving it away.