Okay as I've been sorting out my poorly maintained car, I've taken apart much of the interior and tied down loose things to eliminate sources of noise, and now I can diagnose the persistent noises a bit better.

I'm getting a soft clicking sound that is very much like a loose wire bumping against a panel, but it only happens in 2nd, 4th, and 6th gears. The frequency of the tapping in 2nd seems to match the rotational speed of the 2nd driven gear (a little under half engine speed), while the tapping in 4th is actually pretty similar to the tapping in 2nd. I haven't gotten around to listening to it tick in 6th since I thought of this as it only happens at higher speed in 6th intermittently. The strange thing is that it appears as soon as 2nd gear is engaged, but under engine braking it sometimes goes away, and it doesn't get louder under full throttle. If I push the shifter around, the tapping sound will sometimes get quieter too. It's not loud; when I roll down the window, the light wind noise drowns it out, so it's not like my transmission is making a huge racket to bystanders.

Since it doesn't happen in neutral or other gears, it can't be the engine or rear axle. I was thinking it might be a damaged tooth, but that doesn't explain 2nd and 4th clicking at the same rate. IIRC 6th also clicks at a pretty low rate, when the 2nd gearset is spinning at 7000rpm, which doesn't seem to indicate a damaged 2nd gear. I haven't personally checked it but when I took it to the dealer to do a recall, the inspection said diff/trans fluid both looked good.

Any ideas?

 

I'd get it up on a lift and run through gears while someone else is under the car with a mechanics stethoscope. I'm betting it's NOT coming from the transmission. Possibly the shifter mechanism itself has something dragging against it (looking at you tumbleweeds) only when the shifter is in the rearward position (gears 2/4/6). I bet if you remove the shift boot, console, bottom weather boot you will find the issue.

 

Thanks for the suggestion!

I have removed all the things on the shifter before, in an attempt to find out why my reverse blockout doesn't work (missing spring, shift lever installed wrong), but I haven't gotten a chance to look under the car at it closely. A possibility is something on the engine input side brushing something attached to the shifter mechanism.

 

Okay, figured it out: Shift linkage boot was not fitted properly and was hitting the driveshaft balance weights.