As annoying as it is to keep pulling it out, you have to check between each change. Every time you go to plug in or unplug something.
Swapping the PCMs and getting it to run isn't going to happen, even if that is the issue. The security will have to be programmed by a locksmith. But when you had it able to shift when off, that was a step in the right direction. That's with the new PCM? Is the new WIN from the same van?
Try following the wire loom between those two connectors and look for damage, kinks, newer tape indicating a previous repair, and anything that doesn't look factory.