I've searched and read many, many threads on this topic. Hear me out, this is where I am.

Replaced all 4 shocks, checked torque on all things suspension, sway bar bushings and links are solid and tight. Clunk / knock still there over bumps at low speed.

Jacked up driver side. When holding tire on sides and pushing back and forth hard on rear facing side I can hear the knock! It is coming from under the vehicle in the front center area. What could it be? I was able to put my hands on the front driveshafts where they connect to the front differential and there is some in and out play on both sides, is this normal? If so, any other ideas of what might be knocking/clunking in the front diff area when moving tire like mentioned above? Feel like I'm on the verge of a breakthrough here, but not sure where to go next.

You probably did but torqued everything with 4R on ground right?

What Dil said. didn't do that with my '65 Vette. Big difference.

Yes. When I did the shock install I torqued off ground. Then I realized the mistake and did them on the ground. I've been chasing this clunk for a long time, I'm about to go insane.

When I grab the tire on either side and push on the side towards the back of the vehicle, I can replicate the knock. It's not just a single clunk. Sounds like a hollow bounce with like 3 repetitions, each one fainter than the first. Like a ball bouncing? Also, I can not feel it in my hands on the tire, just hear it.

The really sounds like a bad inner tie rod if it's coming from the center. Have you tried grabbing the outer tie rod end and putting some lateral force on it to see if there is play? You will need to do this while the suspension is unloaded. Try taking a video and posting it.

It could also be loose upper or lower control arms. Make sure they are nice and tight. The LCA's cam bolts should be torqued to 129ft/lb

I have not tried this specifically, but I did grab everything and shook with some force. I will research the outer tie rod check to see how to do it. I'll see if I can get video, but won't be until Sunday.

Yes, torqued them all to spec. Well, 130 instead of 129. Everything really seems solid at the wheel.

My 2010 had the stabilizer bar bushing worn out in the middle that made a clunk over bump or when braking and turning. Easy fix.

Here's a picture of one. Not mine but similar.https://www.toyota-4runner.org/2491937-post13.html

Good thought but sway bar bushings are all solid, inspected them all when doing the shocks. KDSS seems solid as well, no leaks and good movement ion the bushings when jacking up on the front cylinder.

Unless you remove the bracket from the bushings, it's hard to see. When I had the clunk on mine, KDSS was solid, it was just the bar hitting the metal inside the worn out bushing when the suspension was articulating. I had a lot of miles and since it was cheap to replace with 4 OEM bushing I took the chance and solved the issue.

I had the 2 end link bushings and the bushing that is not at the cylinder out. Sounds like I need to check the top of the link bushing and take the bracket off the cylinder and pull that one out as well. Will try this with the tie rod check on Sunday hopefully. Thanks!