3.3L putting out codes P0404 & P0406. Related EGR valve twice but codes return and slightly rough running persist especially under acceleration. Any suggestions?

Those are not misfire codes. P0404 is an EGR position sensor performance code and the p0406 EGR position sensor high. The vehicle needs to diagnosed to see where the issue lies.

You are correct... And I agree!...Thinking 300 series codes!! Still think the scanner showing live data will be VERY helpful.. As part of that diagnosis. I see you are in the same state.. May this is a job for your shop... Don't know how far the drive would be. But the key is as stated a good diagnostic check is a must!