It's been awhile since I disassembled the doors.
I have these clips I took out when I disassembled but I am not quite sure where they go. I think they go on the rod from the lock cylinder where it goes onto the latch assembly.
Can anyone confirm this?

 

looks like a door lock rod clip or door handle rod clip

 

Is there supposed to be a clip on the door handle rod on the side that goes into the lock mechanism? It looked like it just was clipped from the handle side and sat on the mechanism side with no clips.
I think you could be right about the clip going on the door lock rod. There was nothing on there when I went to reassemble it.

 

The door lock clips to the lock lever and rests in the door lock mechanism, as you remembered. That looks like the clip for that rod to the lock lever (at the top).

 

So then I have the door handle rod correct without a clip on the mechanism. That clip didn't go on the door handle rod on the handle itself. The handle has plastic retention clips which I reused.

 

Yeah, the door handle has plastic clips. It is the door handle rod to the latch mechanism that rests in the latch without a clip. Spring pressure from the latch and the door handle keep this rod in place. Door lock rod should have a clip similar to yours on both ends.