Sorry I can't be of more help, I'm just brainstorming here, cuz I don't have a diagram or picture to go by:
The actual lock knob that sticks up from the window sill should just be an extension rod connected directly to the lock. It obviously works both as an indicator and as a way to lock the door manually. Not sure if the lock cylinder mechanism and the door latch mechanism are separate items or if they're 1 big unit. In general terms, the only thing the lock mechanism should be doing is blocking the door latch from operating from the outside.
Can you reach in and manually move the rod that's connected to the lock knob that pops up? Theoretically, this should unlock the door. If you can confirm that the door is unlocked but still can't open via the exterior handle or by pulling on the interior handle rod, then the door latch mechanism is most likely at fault (or the lock mechanism isn't disengaging). Also, if you've pulled on the rod that normally connects the interior handle to the latch and nothing happens, that also might confirm the latch is damaged. Can you get someone to pull on the outside handle while you watch from the inside, to see what's moving (or not)?
OK, just reread your thread... if the external lock cylinder was replaced and does not appear to be connected to anything, its possible that rod could've been left connected to the lock mechanism and is now stuck/jammed in the locked position on the latch mechanism - or otherwise flopping around inside the door.
Any one else have a passenger door disassembled? What year is the X? Not sure if they changed door design with diff generations.