Thunking--leaf springs or differential?

Unless I let out the clutch really slowly, my '05 6spd Tacoma makes a very noticeable thunking sound/feeling. It happens any time I let out the clutch too fast (ie not really really slowly), upshifting, downshifting, taking off from a stop...it happens if I accelerate hard and then let off the gas completely also. At first I thought it was a broken motor mount or transmission mount, but they look good. The u-joints are tight. I then noticed the stock 3-leaf springs are sagging, the second leafs are bent from the clamps out, and I remembered that this truck has 124k miles and about half of those were with a motorcycle in the bed (the bumpstops are polished to a shine). So, I figured that what I'm noticing is spring wrap--these springs have definitely seen better days. However, I just crawled under the truck and tried twisting the driveshaft with it neutral and noticed a fair amount of play (see video). Is this normal? I also took a video of the play in the center/carrier bearing for the driveshaft.

I have had the truck for less than 1k miles and put Amsoil

$29 75w-90 Synthetic Gear Lube - 1 Quart (Pack of 2)

75w-90 in both diffs and the t-case and Amsoil GL-4 in the transmission almost as soon as I bought it. I did add about 1/4 quart of GL-4 to the rear diff because I ran out of 75w-90, but didn't think it would be a problem. At first I thought I just needed to get used to driving the truck because the clutch throw is a lot longer than what I'm used to, but the more I drive it and the more I think about it this just seems wrong. Does it seem like my springs are the problem like I originally thought, or is there too much play in my differential? I'm not new to driving stick, but the only other stick I have driven is a Jeep with double military wrap springs, a 2-inch clutch throw, and gobs of torque, so there are differences in how they drive...

http://www.youtube.com/watch?v=nVqt8QXVD4Q&feature=youtu.be

http://www.youtube.com/watch?v=2JzgSqOnq_w&feature=channel&list=UL

 

I suspect it is your springs and axle wrap. Try this to help narrow it down. Get 4 each 1-1/2 X4 X1/4 steel plates and 4 each 3/8 or larger bolts, nuts and washers. Drill holes through the plates and "clamp" your springs together on the front side. This will make the spring act as one spring and be stiffer. Old drag racing trick.