I have a 350 in my 40, with TBI and it's great. I agree, I love the power and the lack of stalling. I started wheeling with an automatic, and only recently really wheeled with a manual, so I am the opposite as you on that point. I know the manual trans folks like the control they get with the stick, but having the auto is really point and shoot. I do think that you lose some control, but I think that the advantage of not having to clutch and shift roll back, etc. makes up for it (or I might just suck at driving a stick). My tranny is a T350, and I've not had any issues with it. I run an Art Carr shifter and ground off some of the gates. I can't slam from 1 to R, and back, but I am considering it. I am afraid that I'll bump it at inopportune times.
My 40 is on D60s, and stretched to 113 wheelbase. I'll say that while I like the stretch, my driveshaft takes a beating on the rocks because it's long. That being said, whomever built my truck left me with a crappy pinion angle that I am going to have to correct at some point.
I've enjoyed reading this because this is my first hardcore rig and I am still learning it and all the mechanics of it. Plus if I ask a dumb question or say something stupid, everyone will know why.