[chrisktx]

I will try to clarify (excuse the pun) and answer some of your questions

DrDave, You've been very helpful!

Noise: In flight only, only during transmission and reception...all other times its clear...its almost like the squelch gets magically pulled during any transmission or reception (both near and far) in the air... then magically pushed back in when the frequency is quiet. In flight radio checks are loud and clear, with some noise going through out headsets.
If a lot of traffic (close and distant) on com, we get that dreaded squelch sound to go along with what they're saying...
I actually pull the squelch and the sound is the same.
What gets me is the to different radios 12D and 12E. Because the sound is exactly similar (with two different PMA 340 audio panels) I keep leaning toward airframe noise. Yet the ambient noise is nice and quiet.
Still... the filtering on the audio output caps you mentioned I'm going to pursue, I'll call my radio guy and see if those were replaced.

To answer a prior question on 3/13: Sound is exactly alike when I switch one radio off, one on and vice versa.

Popped the cowling and took a closer look last night. I need to correct myself: The P leads do have shielded wire, in fairly decent shape.
I looked at the alternator, no filter there either. The rear alternator has easy access, the front...oh boy...Looks like I'll have to dissect the engine to get access.

Will fly with a handheld this weekend and see what kind of noise I get...sure wish I had the adapters for a headset to plug into it.

As for running the radios on a separate power supply for testing, that could be a bit of a challenge but sounds like a good idea

As for disconnecting one antenna in flight to see how the other radio sounds:
No change on the other radio

As for the Nav, I've confirmed the squelch/Ident isn't on. Need to test that end more.

I did have something weird happen, every now and then (twice) at the very end of my transmission, things get crystal clear and louder, it only happens for a millisecond, I have not been able to replicate but it has happened only twice...it seems to happen during slightly longer transmissions. Houston approach confirmed it while I was transmitting to them the first time it happened. Two flights later, it happened again. It's almost like the PTT gets a good connection when you hold your mouth just right, but I can't confirm. I shot it with cleaner, turned the button to break up the crud, etc.