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I did the swap from a 22re to a 22ret a few years ago. I just had issues with blowing head gaskets.
Just a thought for you: When you did the swap did you get the turbo computer from the turbo truck to replace you regular ecm? Also make sure you have no leaks from the turbo to the intake. It wont appear as a vacuum leak it will be more of a pressure leak especially under a little boost. If the air line from the turbo has a crack or small leak it will cause it to not run right. With the one I did, my turbo line came off under boost and the truck would barely idle and when you gave it any gas it would die.
This may help it may not.
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