I totally understand your reasoning.I'm pretty sure the 6.7L Cummins conversion will happen within the next 1.5-2 years but I won't be going with a manual trans. I had a Super Duty truck with powerstroke/6-speed combo and I just didn't enjoy driving it. My friend's Dodge wasn't any more enjoyable...probably even less so. I personally just don't see that a manual offers any advantage for how we are going to use our van. It would actually be a nuisance because my wife would refuse to drive and I'd be stuck behind the wheel every time we went out.
I'm in the information gathering phase right now. Trying to decide which trans I will go with and how I am going to integrate all of the electronics. I'm also keeping my eyes open for deals on parts I know I'll need. Not much else can happen on the project without spending a van load of money though...