Drive Axles thunking?

[Delorean17@xxxx]

HI,
Every time I take a corner in my car I get one "clunk" coming from the 
rear of the car. I checked the trailing arm bolts and they were tight with 
no shims missing etc. so I ruled that out.
Another member on the DML (thanks Jim) told me to check out my axles as 
they can cause the clunking noise I am describing. I jacked the car up to 
find that one of the CV boots was missing and 2 others were torn pretty good. 
When you grab on to them they move back and forth and make the clunking 
sound which I am probably hearing while turning.
Today I removed the axles as I am going bring them in to be cleaned and 
repacked. Should I just pack them up with grease or did I most likely cause 
other damage by running it W/out the CV boot?(at the most the boot was 
missing for 3k miles as I checked it at the last oil change and it was OK) By 
the way this car is an automatic.

Any info would be greatly appreciated.

Thanks
David