There are only three you have to worry about.
All three are on the driveshaft, one at each end(U-Joints) and one in the center. All you have to do is crawl under there with a grease gun (loaded of course) .
Grease the U-Joints until just a little grease filters out. The center one reqires a little more that a few cranks. Just look for the tiny nipples (sorry),those are called fittings or zirx, thats where the grease goes.
That "should" take care of the clunking sound when you shift.
Good luck!!
John