You know Frontier719, I bought a 2000 4runner 4x4 with 111,000 miles on it last September and it makes the same clunk you are experiencing with yours. I also have changed my transmission fluid and all my u-joints and slip yokes are well-greased.
I've spent some time trying to diagnose what's causing this, and I think it's just the fact that sometimes the transmission hasn't dropped into the lowest gear before coming to a stop. After you left off the brake and start rolling forward, the transmission finds the lowest gear and drops in giving you that clunk feeling. What I've noticed is I experience the clunk after letting off the brake if I come to a stop quickly and didn't give the transmission a chance to make it into the lowest gear yet if that makes sense. To see if my theory made sense, I would drive through residential streets and come to a slow stop giving the transmission a chance to drop into the lowest gear before coming to a complete stop and I wouldn't get the clunk after letting off the brake. I keep my hand on the shift lever and I can feel the transmission dropping into gear when I experience the clunk.
I understand some think it's a driveline issue but I truly believe it's just a situation where the transmission hasn't dropped into the lowest gear yet. The lowest gear on these automatic transmissions is pretty darn low. I detect it shifting up into second at around 10mph. That means when it's downshifting, it's not going to drop into that gear until you slow back down to around 10 mph. If you come to a complete stop quickly, I just think the transmission didn't have a chance to shift into the lowest gear yet. Taking the foot off the brake and rolling forward allows the transmission to finally drop in.
I've never experienced this with an automatic transmission and it possibly means that maybe we both might be having to do a transmission rebuild or replacement at some point. My transmission has no problems shifting or downshifting and I don't detect it slipping at all. It's just that weird clunk I feel at a stop sometimes. As long as the transmission isn't slipping, I'm not too concerned about it but it would be nice to get a definitive answer what exactly is causing this. Since my 4runner had very low miles for it's age, I think most of it's miles were around town and the transmission probably got a lot more shifting through the gears than one that was driven on the highway mostly.
Does anyone else have any theories on what we're experiencing?