Weird Noise When Shifting
 

I am having a weird noise every time I shift from 1st to 2nd to 3rd. Seems to be happening only when driving. In neutral or with the car off, the sound does not happen. It sounds like it's coming from the rear end and is only on up shift. Haven't heard it from downshift.

I have jacked up the car to see if there is anything hitting but it all looks clear. Only thing that has been changed late last year was axle replacement but that was done about 5-10k miles ago. No marks on the driveshaft that indicates it is hitting the shifter (would also feel it).

Below is the link to the sound which you can hear clearly the noise around 4 second mark and the 8 second mark.

https://streamable.com/rvyypd

Any ideas?

What's your milage and bushing mods? Might be worn out drivetrain bushing, particularly diff carrier. I'd inspect them all - transmission mounts, shifter carrier, driveshaft cradle, diff carrier, rear subframe bushings and all suspension bushings in the rear.

118k miles. Only roll center kit and the TRD quick shifter. I thought I put that in my op but I guess I was too sleepy while typing this. The quick shifter mount/rubber grommet that replaced the bushing looks good still when I checked. Maybe one of the rear diff bushings looks like it needs replacing but not immediately. A bit worn but not to a point where deteriorating.