The passenger door won't have any effect on EKA entry.
If you can unlock the drivers door with the key, but none of the other doors unlock (aka the central locking isn't working) then this is NORMAL. Also it is somewhat normal for doors to go into superlock mode when the BECM goes into lockout. You should always be able to unlock the drivers door as it is a mechanical link between the key lever and the locking mechanism inside the latch, but other doors may or may not open depending on whether the superlocking motors actually still work.
Normally, if the EKA will be accepted in the drivers door (which yours isn't - either because the BECM has corrupted it when it's gone into lockout, or it's just simply the wrong code), on the final turn to unlock, ALL the doors will then power unlock, and the central locking will start working again, and allow you to start the vehicle/sync the key etc. At the current point in time, the other doors not responding is NOT a fault with a latch or anything like that - rather it is a sign that the BECM is locked out.
So I would hold off on the passenger door at the moment. If your drivers door lock all checks out, then I would get that back together and back in the vehicle. Your BECM is in lockout. You may get lucky and be able to recover it with the Nanocom when it arrives, but if not, then it is really starting to sound like the BECM is in an alarmed state, and this will require advanced diagnostics to connect to the CPU on the main logic board and reset the lockouts.
Sorry I can't offer any more good news than that at the moment - but everything you've mentioned and the fact that your door lock checks out, and the fact the other doors aren't doing anything all points to it being a BECM lockout issue, and I doubt the Nanocom will be able to solve this for you, especially if it's a V35 board that you mentioned earlier.
Marty