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Interesting dilemma. Engine runs great when you first start it but when you put it in gear after a short period of time it begins to sputter and misfire. Ive checked the egr and its fine, the timing is fine. The only thing I can think of is the engine is sucking up transmission fluid through the modulator if that's possible. Its a little cold here at the moment so I will have to wait to check it.
You would notice some smoke if the modulator was bad and fluid was passing through it. This would be white smoke as a matter of fact.
Chances are that you have poor timing, or a simple vacuum leak.