There is a guy who lives about 6 miles from me who runs a repair business from his house. However, he is listed in Minn Kota's book as an authorized repair facility. He is located in Prattville, AL. I'm sure you can go online to find the nearest authorized dealer to you.
The shaft warranty is transferable from what I was told. Though after the 3 years you are on the hook for labor. And as far as running the ducer through the shaft yes that would void the warranty