Sorry if I'm confused, but you're saying that the car WILL start but only if jumped...and that you've tried 3 different batteries in the car, but car will not start if battery is directly connected? If that's the case, what happens if you install the battery from the jump in the car? I know this seems overly obvious, but I'd assume it would start...then you could go about trying to find the point of issue.
If car does start via jump (connected at battery), I'd rule out immobilizer issues (as well as other components in your schematic) and start thinking about wiring and connections. My fist thought is a braided wire that a few strands have broken free...thinking that an x-gauge wire can handle x-amps, but if at the point of connection the "strands" are not all making contact, the x-gauge wire is effectively 1/10th x-gauge and thus not sufficient.
I know you have done your homework and are way down the diagnostic path, but perhaps you should try to "restart" your approach and clear any potential misconceptions. I know I am the biggest victim of "thinking"...many (many, many) times I have a hypothesis stuck in my head and spend far too much time trying to prove I'm right rather than taking a few steps back and starting from scratch...even then I wouldn't admit I was wrong, just not right enough.
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