what would i have to do if i want to go from a inline 6 with a manual Transmission to a 289 with a automatic Transmission.

Find an engine and transmission and install them. You will need the correct motor/transmission mounts but that is about it. Clearly you will need the exhaust and to hook up engine cooling and electrical but it should be an easy swap. The front springs may need upgrading and you should look into a disk brake upgrade for safety.

I did forget that the 6 cylinder cars have the 4 lug wheels. I would upgrade the front hubs and the rear axle to V8 spec.

I upgraded the front to disk brakes but it was for the inline 6 manual, do I have to change them?

Not really sure about that. Take a look at the website for the maker of your kit and see if it applies to the V8. Hopefully all you have to do is swap the hubs to 5 lug.

https://www.cjponyparts.com/resources/v8-swapping-classic-mustang

I am a purist so I would sell the 6 cylinder car and buy a real V8 car. You will probably devalue your car with this swap.