Okay, here's the update. I changed both drive shaft u-joints. They came off fairly easily after spraying with PB buster. Put everything back together and greased up the spline shaft real good with hopes of eliminating the clunk when shifing into drive and all is well. After picking up parts for $41 from O'Reilly's, I stopped at a repair shop to get a quote on changing them. They wanted $265 + tax.

Take a look at "U" joints, CV joints and motor mounts.

There is some sort of joint inside a boot. Is there anything that can be done to check if this is worn. I can't find anything in the manual reffering to this part and it seems that the whole shaft will need to be replaced.

I believe the "some sort of joint" is a constant velocity U-joint, aka a CV joint, and they are very expensive compared to standard U-joints. They also require replacement of the entire shaft, as you surmised, no doubt accounting for at least some of the price difference. A previous poster notes paying $41 for a pair of regular U-joints for his CRD. I do not know what the specific on you are talking about costs, but I can tell you that I've had to replace CV joints on other vehicles, and have paid as much as $1,000 for them. It should be noted that one should inspect CV joint boots often, and if you find one with a torn boot, it is relatively cheap to repack with grease and replace the boot, but if you let one with a torn boot go, in a year or so you are going to have to spring for the joint replacement.