Curious, but could the electrical systems of older cars just not be up to the task of carrying enough consistent voltage to adequately power these modern computer-controlled engines?
Is there a way to test the crank/cam sensors out of the engine to see if they are still good? For that matter, what would cause them to become "bad" from sitting in the first place?
What I think the difference is Tom is that stock Dmax equipped trucks have the batteries right near the ecm, starter, and fuse box. The cables also have a separate lead to the fuse box in a stock application. So they are getting the direct voltage needed to run everything.
When running a single battery in the rear and long cables to the starter, then running the power leads for ignition and ecm off the starter (because it's easy) and the ecm cannot power everything up when cranking.
These ecms are very finicky when it comes to voltage and grounds.