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I had a similar issue with my 3.0 truck. I'd replaced the engine, and was having charging system/starting issues. It would run perfectly for awhile, and then die. I tried multiple batteries, multiple alternators, and even 2 PCMs, and the problem was present throughout those various iterations. I couldn't find any loose grounds. After fighting it, and throwing parts at it for a couple of months, I broke down and took it to the dealer. An hour later, my truck was fixed. When I reinstalled the engine, I had snapped the "42 Pin" wiring harness connector back together, but I'd forgotten to tighten the bolt that runs through that connector, and it wasn't making a good enough connection. It was starting, and running strictly on the battery. I felt like an idiot, but it's been fine ever since.
The moral of the story, is that a loose/bad electrical connection can definitely cause starting issues, or charging system problems. Sounds like you've found a potential cause. I'd go through and double check every electrical connection you can find in the engine bay just in case.
