I think there's a thread on this forum about the cables/wires inside the door panel...hitting against the panel or door frame causing some noise...also, I believe there is a thread about some wires behind the headliner by the driver's head causing noise as well. You should be able to search for those.

As for me...I had a very slight ticking noise that seem to come from the upper door panel near the b-pillar. I had actually removed the entire door panel and wrapped all the cables and wires in foam...but that didn't help.

Try this...find a section of road where you know the ticking noise always occurs. Make sure it is safe...when the noise starts...take your right hand...and press your fingers inbetween the upper door frame (about midway up the window) and the rubber weather stripping. If the noise goes away (repeat several times to make sure)...then you door needs to be adjusted inward.

If you look at your latching mechanism...you have the latch on the door and striker 'U' bolt on the b-pillar frame...if you feel comfortable with it, you can adjust the stricker bolt inward so the door closes tigher to the body. The ticking noise on my 4runner was actually caused by the latch moving around the striker bolt.

Now, I actually did not adjust the striker bolt...what I did...for some reason, I had some old rubber door stops laying around...I found two that were slightly taller than the door stops on the 4runner...so, I just replace the stock door stops with these I had laying around...the noise went away...except when I take sharp turns...

The rubber door stops (not sure of technical name) are located outter edges of the door frame...one about halfway up and another at the lower corner...be careful removing those...its a pain and you could scratch the door frame.

An alternative that might work is to get some rubber self-adhesive pads and stick those to the body frame where it meets those rubber door stops.

good luck...