On my truck we couldn't figure it out for the longest time, but it was the 2-wire harness that goes to the positive side of the coil. It would stall and backfire and run only when it seemed to feel like it. That wire had to be in just the right position or else nothing would happen.
It's so stupid because the wire makes such a wicked angle from where it comes from to where it enters into the coil. Right beside the exhaust manifold too, no wonder it went bad. We thought it could be everything from plugged injectors to bad fuel to no fuel, we were so stumped. All it was was that stupid wire harness. It could be anything on your truck though, but make sure to check that piece out.