OP, i have 4 friends with 5.0s, 3 have manual trannys and after about 5k miles ALL 3 are having issues. They been researching and it appears that the manual tranny in 5.0 is fairly poor and has ton of issues. Sure, you're covered under the warranty but what do you do once warranty is out?
In 5.0s case automatic transmission is better and performs better. My friend Matt with intake and a tune ran 11.92 with an automatic tranny.
Another friend has a '13 5.0 with 800 manual and just went into shop for tranny problems(dont know all the details yet)