If its like previous VW trannies there could be an issue with the Mechtronics unit , apparently it controls the gear changes . we had similar clunking in our older T5 with the Tiptronic box . Lumpy up and down shifts from 3 to 4th slipping at times as well the valves become sticky and cause problems . Has it had a second service and filter changed ? as they are supposed to be done at 60000 kay intervals and YOU have to ASK for the filter to be done from what I have read . In ours the filter had become blocked and was stopping the fluid from getting to the clutches etc which caused complete failure , the people who did the rebuild had problems with the Mechtronics unit and it still has a slight lumpy change now in 2nd and 3 rd . This may help understand the way it works scroll down to see the pros and cons. https://en.wikipedia.org/wiki/Direct-shift_gearbox
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