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Is your tune a commercial tune or is it a one off tune? If your tune was done by an individual instead of a commercial product, the person who tuned it might have caused your problem by accident. If a commercial tune, then there is not a big chance the tune is causing the issue.
I see that you said the problem started before the tune. I would still look for something accidentally unplugged or a broken wire. EGR deletes are not known to make a car run worse. Once you get everything reconnected you will know. But, you will need to remove your EGR delete tune to be sure.
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