1989 Ford Ranger Clunking noise when shifting

My truck makes a loud clinking noise when I am shifting from drive to reverse and when it changes gears. It only does it once in awhile. I looked underneath and where the drive shaft enters the tranny there is about a half inch of clean shaft. I don't know if ther drive shaft has somehow moved back or if there is a missing seal or something. I had a rebuilt tranny put in about two years ago. There is no play in the drive shaft or u-joints. Is it a problem I can fix or is it expensive?