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Hello, do you have a way to test for codes?
To me with what you are describing sounds like you have an issue with the EGR valve. The EGR valve is very well known to act up and stick once the vehicle warms up. It is usually pretty good about setting codes but it doesn't always happen. That is what I would suspect as being your issue.
That still sounds like an EGR valve to me that is acting up. That is how the vehicle will act when they fail.