I would not do the footwell pods or defrost pods if they are working. You can change those without removing the dash. If you pull the dash, you should change all the pods that *require* dash removal... that would be the center vent, diverter, and both recirc pods. I just ordered all four of these last week to replace on my 300E, current cost for the four is approx $125. Not cheap, but worth the trouble, IMO... especially if you live in a warm climate!!

I'm not sure what would cause the thumping, but if you are getting very little air from the center vents, it's pretty likely the pod is toast. You can verify by testing at the 7-port manifold behind the glovebox though.