My clunk is gone as of five days ago. I was researching the many posts on here about it.... One post in particular basically implied that not enough grease was being pumped into the slip yoke zerks. This person talked about 15-20 pumps (or thereabouts) but the key was doing it until you actually saw the silver part of the metal shaft MOVE! Then he pumped a few more in there.
This got me wondering - I bet I didnt put enough in and if I did maybe thats the answer and I just needed to be pumping more.
I got under there and hooked up my grease gun to the front zerk and watched the shaft pumping in grease one pump at a time.... FINALLY after about 15 pumps I saw it! The shaft moved out about 1mm ... each pump after that I saw it move another millimeter... I proceeded to pump 4-5 more pumps until the shaft had moved about 1/2 to 3/4 inches from where it was. I did this because I wanted it to have a little extra logically assuming the thing was way under greased if it took that many pumps.
Then I moved to the rear wheel drive shaft and repeated.
Again, it was about 15-18 pumps of grease before i saw the shaft start to move. Same thing... 4-5 more pumps until the shaft moved out about 1/2 to 3/4 inches from where it was.
Went out and drove the 4r..... AMAZING. Even the brake pedal seemed slightly firmer, to which I dont have any understanding of why, but the clunk was GONE.
The next day, I threw it in drive from park and it went clunk, so I took the opportunity to go exercise the gears a bit (just made sense to me) so I went into reverse, backed up 3 feet, applied brakes, went into drive smoothly, rolled forward 3 feet, applied brakes, back to reverse.... you get the idea, a few times and soon it was even moving R to D very smoothly... I feel like I was distributing the grease....

This is unrelated and not required, but just sharing what I did thinking I was helping with the grease distribution faster.
Anyway, its been days now and my 4r is not clunking when I come to stops while driving and not clunking when i let off the brake at stoplights anymore at all.....no one "tapping me from behind".... makes me want to shout to the rooftops... GREASE GREASE GREASE and make it go away. If you have a clunk, maybe you just didnt grease enough... grease until you see the shaft moving with each pump.
Now, will nirvana last for me? I dont know. How long? I dont know. But the clunk I had when I got the truck 3 months ago and have been living with consistently is now gone just from putting ENOUGH grease in there. if it comes back I may assume the grease has been distrubuted and it needs more.... and if so, I will repeat the process again until I see the shaft move once... I assume and think at some point if it comes back, eventually I will grease enough that it will be full and I wont have to do this as much if at all.
Do you have the clunk? Thunk, tap, lurch, or whatever you want to call it???
Go do what I did and report back!!