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.

 

Could be as simple as needing a tuneup? Best thing you can do to these trucks is give them regular tuneups unless you have already done one recently.

 

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.

 

You have a vacuum leak. If it was a timing isue, your truck would be hard to start.

 

Not necessarily.