It has been my observation that plain diesel fuel is just inadequate. You're most likely dealing with partial injector clogging and low-cetane fuel. The solution may just be using a good injector cleaner and cetane enhancer. I don't recommend dumping ATF in the tank. Is it nailing at idle or while cruising?

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2004 VW Jetta TDI (manual)

Past MB's: '96 E300D, '83 240D, '82 300D, '87 300D, '87 420SEL