Greg, I'm actually in the process of piecing together this setup. I still need to find the small details such as what pushrods to use, and what can be done to lower compression ratio. Either thicker head gaskets or opening up the combustion chambers themselves. Ive heard Moe's performance has some input on this.
As for the intake port mismatch, I've got the 6.1 intake manifold. And as you mentioned before, the exhaust port can be solved by opening up the header.
I'm having trouble finding the A/C and Alt. relocation brackets, another key element for installation.
There was a guy on DT I met a year or two ago that ran an entire 6.1 top end on his ram. I can't remember his name and haven't ran across him anymore.
So far I've got the intake manifold assy, and heads. So I guess the main hardware is taken care of.
Also, SUPER anxious about your megasquirt installation!