Ok, here is an update. I was correct, the shock was not centered in the mount when removed. It didn't fix the clunking though. Good news for anyone thinking of trying, i found a way to do it without modifying the stock components. I went to Lowes and got two different sizes of rubber bushings.
I put the 15/16 bushing over the threads, the opening in the shock mount is 1" so this bushing fits inside of it. This keeps the shock centered in the mount, and since the I.D. is 3/8" it fits over the threads without using the sleeve bearing from the stock bushing. I used the larger bushing on the top side of the mount, it doesn't fit thru the opening. I did have to cut the nub off of it. Top it of with a washer and cap nut.
So I got it centered in the mount and tightened up. My only complaint is the height of the 15/16" washer, it is slightly higher than the mount, so it doesn't clamp down on the mount until you tighten up the nut and compress the bushings.
The clunking is still there though (see video link). It could be because of that bushing height, but I realized it have metal-on-metal where the boot cap meets the shock mount. I think that is causing the clunking. I plan to put a rubber or neoprene pad in there for an isolator. I will also put a thinner bushing in the lower part if I can find one.
Now for the ride. It now feels like a lowered vehicle, the back is somewhat bouncy. A couple of times it rubbed the tires with my 100# daughter in the 3rd row. I couldn't really feel a difference in the handling unless it is a bumpy corner, then it bounced. What would be perfect is a modified shock mount. We could use the stock load-leveling shock, but reduce the height by an inch. I really like the feel of the stock shock better!
To be continued...