Honestly it depends on budget, what your goals are, ability, etc...
For my goals I went with a Drive By Cable setup and a 2001 suburban. It was a 1500 so the trans was a 4l60e. My original plan was to use an nv3500 5spd with a manual Tcase. I will be going to that after I get everything driving how I like.
I can't stress enough that the Body lift made everything easier. Just having room to work and mount everything was well worth the investment.
Engine management, if I could do it over I would go with the holley Sniper system.