They don't go well together. Like Shabby said, you can get 23 PSI with the tune. If you hold that over 3 seconds, you'll go into limp mode.
I had the mod on mine when I got the tune and noticed some knock at 23 PSI. I backe mine back to the stock position, get 21-22 PSI consistantly, and eliminated the knock.
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I have the rod mod right now just getting the info together fo rthe tune. Didn't want to conflict with anything. I will turn the rod back before the tune then.