Alternator Noise

Yes I agree. Since the OP said the alternator noise was only noticeable through his West Mountain speaker, I assumed it was the speaker cable picking up the interference. Of course he can't hear the whine through the speaker unless the volume is turned all the way up. So it sounds like he's maybe worrying about nothing.

 

Where's Slowmover?

He's the West Mountain guru, but haven't seen him around for a few months now.

 

Well the thing you need to know (if you don't know this), is that the RF gain effects the volume in the radio, and therefore it will effect the volume in the external speaker too. You say by turning down the RF gain, and having the clear speaker filter out the static from the radio (squelch circuit), that's really not the job of the clear speaker. It's job is to reduce the electrical noise (not eliminate it per manufacturer), the key word is "reduce". I don't have any personal experience with this type of clear speaker, so I did a quick research on a well known website of product reviews. One fellow had a 60hz hum with his speaker, and the manufacture company sold him a $40 line insulation to install in the audio cable, but it didn't help. Another fellow was having ignition noise trouble, and the only thing that would help eliminate the electrical noise, was the noise blanker on his radio.
At this point, I think the best thing to do is try the toroids when you can get them installed and see if it works. Otherwise you may have have to try using a shorter power cable going to the cigarette lighter just to see if that eleminates this problem.

 

EMI vs RFI
Doesn't filter RFI
EMI / RFI Frequently Asked Question