You may have more than one issue going on.
Drive line clunk-thunk:
Best way to diagnose drive line clunk-thunk. Is while driving about 35MPH let off the gas pedal, CLUNK. Then without delay, press the gas pedal again THUNK.
The video makes a few mistakes in lubing the forward & aft propeller shafts (aka drive shafts)
- Moly grease is fine for the slide yokes (aka u-joints). I do use moly for very difficult cases of drive line cluck-thunk. It can help reduce stiction. But in most cases I do not find molt necessary.
- Typical moly is not the best choice for high speed bearings such as the spiders (aka U-joints). Moly retains heat.
- In video he has the vehicle jacked up. This fully extends slide yokes. Which note how we can see silver or clean parts of slide yoke. So that when lubing while extended, the cavity becomes over filled. Once lowered to the ground, this over pressurizes the dive line. This can put excessive pressure on the transfer case and differential. If lubed like this (raised vehicle), we remove the grease zerks from slide yoke, then lower to the ground. This allows excess grease to flow out.
- If slide yoke seals worn out, the grease will pass seals relatively easily. With good seals, which is indication of properly serviced propeller shafts, they don't easily allow grease to pass. In these I've special techniques for lubing when very dry. But safest is to go with Toyota's new recommendation. Lube until extension of yoke just begins and stop. This is with weight on the wheels/tire. So that vehicle is in it's neutral stance.
D-N-R clunk:
This is most often associated with worn out front drive shaft (AKA CV"s) axle and hub flange teeth/splines. Easy test for this:
New for comparison.
There are other bushing that can cause clunk. But you'll chase forever if above aren't corrected first.
Transmission:
Toyota changed the fill procedure for the 04- up. Basically we now add more fluid, than was factory filled to top off.
With transmission & Torque converter (TC) issues, we typically see is RPMs go up and not corresponding movement. Not so much a jerk. Transmission and TC can causes a jerk. But most times it not just on take-off.
They will slip or jerk between each gear typically. This is most associated with low or bad fluid.
Or they just refuse to move vehicle in either a forward gear or perhaps reverse. Shot transmission, not common in properly maintained!
Or have a shutter in certain configuration. Low fluid or moisture in fluid.