Low RPM Engine Rumble

About a month ago, CEL came on for a misfire P0303. We took the EGR system out and cleaned it thouroughly with power washer, etc. The cooler, the EGR, the pipe and the intake manifold were all cleaned. The cooler was very clogged, but looked good when we put it back in. Also changed the spark plugs and the ignition coils. Car has about 80,000 miles.

Fast forward about a week, and we started to get an engine rumble at low RPMs usually as we take the foot off the gas. The rumble appears to have gotten worse and more frequent over the last few weeks.

Oil consumption is minimal, coolent levels are good and not dropping. We've tried disconnecting the EGR system plug, CEL came on (as it should) but the rumble remained. Other than that, no CEL. Gas mileage still decent, over 48 possible with a little effort.

Any thoughts? Could we have dislodged some gunk that is clogging up somewhere? What are the next diagnostic steps?

 

Also, I forgot to ask, what is the time frame that this becomes dangerous to the longevity of the car?

 

The P0303 was solved by cleaning the EGR, the cooler, and the intake manifold.
We haven't had any misfires recorded since then.

The knocking at low rpms was not occuring at all before we cleaned the EGR. Now we are experiencing knocking when we ease off the gas. This is brand new behavior that we didn't experience at all prior to the cleaning.