So I have a clunk when shifting from park to reverse or drive. I have read multiple posts that the most common cause is worn out u-joints, but when I crawl under the vehicle I could not see or feel any play in any of the joints. I also regularly grease them every 10k miles.

I'm wondering if maybe it is the transmission or one of the diffs. The weird thing is, when I cold start the vehicle and shift into R or D the clunk is completely gone and it is very smooth. Only when I have the vehicle up to operating temp the clunk comes back and is obvious. If it was the u joints I would expect it to do it all the time? I have also read multiple threads about people complaining that their vehicle shifts hard when cold and smoothly when hot, but mine seems to be the opposite of this.

Here is a video of mine that I filmed from different angles. Maybe someone who has knowledge can tell if anything is moving too much/has abnormal play? Any advice is welcome and I would greatly appreciate anything. Thank you

3rd gen 4runner clunk when shifting - YouTube

I had a similiar clunk and it was due to me putting too much grease in the slip joint zerk on the rear driveshaft. To fix it, I removed the slip joint and cleaned out all of the excessive grease. I then just brushed on some grease onto the teeth of the joint. I also left the zerk fitting out until I found a "breather" fitting to replace the zerk fitting. Basically too much grease doesn't allow the joint to move back and forth easily which can cause binding in the drive train. This has been a problem with other people as well. Mine hasn't clunked once since I made the changes.

May not be your "clunk" but it's worth taking a look at.

I will definitely check this out today. What is the breather replacement you are talking about?

I watched your video and that is a normal amount of rotational play due to the backlash in the rear differential gears.

Something like this:

https://www.amazon.com/Buyers-Produc...%2C357&sr=8-26

A member on here gave me mine so I'm not 100% sure the one I linked is the correct size but you get the idea...

I took the driveshaft apart and greased it well but the sound still persists. Does anyone have any thoughts on why it would only be present when the truck is warm and NOT present when cold started with higher engine rpms?

i have the same noise and it even feels like it sort of pops into place when going from drive to neutral/park/reverse. same experience?