ls with 4l60 is what ill run in mine for cost and adaptability (Ill run a 241/300 doubler but have the option to adapt to toy cases)
the 6l80 is a very big trans and the pcm is the valve body and pretty much has to be replaced if a failure happens. (my experience is only as a gm tech so no aftermarket parts/tuning systems)
Yes, you have to run a high speed carrier (3.73 and down) with the jk gears in a standard 44. The 6l80 is out of my price range
i priced out a 3 speed hero case and was blown away how much it was going to be with exchange rate and shipping 8600 canadian ... my wife would shoot me if i dropped that kinda cake on a t case..
What trans and ratio atlas are you running now? Is your 6.2 stock or have you done some upgrades?