In case it helps, I found this tech sheet to be helpful when tearing apart my doors: 96-02 Toyota 4Runner Factory Service Repair Manual

I was working on my front driver’s side door yesterday (different issue - will lock/unlock, but power locks don’t work, even with a new OEM actuator).

From what I remember, the rod from the lock/unlock clips to the actual locking mechanism itself, and has nothing to do with the actuator. The actuator has a little tab on the end (the part that goes up and down when activated) that is inserted into a spot on the locking mechanism, which locks and unlocks the door. My bet is that your issue is with the mechanism itself, not the actuator. There is another rod that goes from the door lock to the mechanism - is this one in place? If not, that could do it.