Yes, there is a U-joint in the middle. There is also a rubber-mounted support bearing in the middle also. Try moving the shft up and down and see if there is any play in the lateral direction also, the rubber mount can wear out and make noises as well. I am not familiar with the TV cable misadjustment causing a clunk when put into gear. It MAY be the cause, I've never heard of it before though. Usually a maladjusted TV cable will cause complaints of either early shifts or late shifts. The bowden cable (TV cable, meaning throttle valve cable) should have just a slight amount of free play to it. Not extremely loose, and not pulling on the cable at all. MB does allow a certain amount of adjustment to be performed outside of this parameter to tailor the shift point to the owners desire however. But if it were "way" out of adjustment I would think your shift point complaint would exceed your problem with the clunk, so in general I would think of other solutions.
When Steve was coaching you on adjusting the vacuum modulator, were you trying to make the shift harder or softer? Any chance it's adjusted a little too hard now?