BeansNcornbread

I'm looking at doing an engine swap from the stock 4.6 to the 2013 or 2014 5.0 Coyote. I know the engine will fit, but I'm not sure about transmition fitment. I'm not sure if purchasing a stock 2014 GT transmition and shifter would line up with the stock hole where the manual shifter currently is, or if I'd have to make some cuts...
Something like this isn't common for my year of Mustang, so I haven't been able to find much help.