I went through the same thing on my 91 300D when I got it. I had injectors cleaned and checked and same thing. I did a Diesel Purge and while the purge was running, the engine was as quiet as a gas motor. That told me it was not a mechanical problem but was nailing. I haven't messed with it since. It runs good, gets good mileage (If my wife drives it, not as good when I drive it). Try Diesel Purge and see if it is quiet while running on the purge. If it is, don't worry about it.

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84 500 SEL (307,xxx miles)