Persistent Engine Noise

No one on this forum can say with certainty what your issue might be because it is impossible to do via the Internet.  We can only make suggestions, which you have followed pretty well.  I suggest you may need to take the car to a good professional automobile electrical shop in your area and ask them to run a full set of diagnostics on your electrical system with special attention to spark noise. How new are the spark plug wires, the distributor cap, and the plugs themselves?  Sometimes all you need to do is a complete engine tune up.  It is also possible your ECU is bad or has a bad ground, and a good shop can test for this too.

Finding and fixing ignition system noise is maybe one of the hardest things to do in car audio, and I know several people who trade in their cars for a different model once they realize how difficult it can be to track down.  Expect to spend some time and money if it's in your ignition system.

ha! I've already considered trading mine in too! unfortunately, I still owe a good amount on it. This is a 2007 Ion with 31,000 miles (I work about 60 miles from home) purchased new in October 2006. So everything on it is pretty new. Prior to making that move (and after much deliberation today), I'm going to exhaustively go through the entire system, essentially take everything out and reinstall, just to make sure there was nothing simple missed, nothing overlooked, looking for good and bad grounds, etc. When everything checks out and nothing significant found, then a check by an auto tech will be left. I hate to bring it to someone and spend the money and then realize it was something simple all along that I could have found if I had reviewed everything. When I get done with this check, I'll post back.

Not necessarily, although this does point to the alt or the voltage regulator.  But modern cars work in mysterious ways.  You need to go visit a good auto electrical shop and get some testing done.

Well, like I just said:

Yes, i read that the first time and am going to have the alt and other items looked at as soon as I can afford it. The post I made about the muting plug was an topic out of curiosity and not something I intended to be about my car per se. I thought about it after reading Forbidden's info about muting plugs. It may be more helpful if it was left as a new topic instead of bringing it in here.