Side note for future reference. The nagging CEL I mentioned was related to the egr. Even after reinstalling, I kept getting the same CEL. It ended up beeing the result of an earlier AEM map where I was clamping the map signal. The ecu performs an egr test where it expects to see a slight drop in the map reading under certain conditions within a specific rpm window. I had the area of the AEM map where this happens clamped too low and when the test was performed, it didn't see a change and boom. Once I realized this, it was a 30 second fix!

Just thought this might be useful to someone in the future.