The new alternator came in yesterday, good news.
At one point we had an output of 14+ volts on the original alternator. This morning the alternator read 13.5. Last night I went through the entire charging system cleaned every contact that had anything to do with it the batteries and alternator. That included both engine grounds and the driver's side was a lot of fun (that right there was sarcasm in case you didn't catch it).
Nothing has changed, I'm still running a high idle anywhere from 1300 to 1500 rpm. I am thinking that the engine computer is taking the reading off of the alternator itself, because the batteries are up. The last time I checked they were about 13.7 volts (because they're new batteries).
Unless that alternator is not charging because the batteries are where they need to be and the voltage regulator (which I assume is inside the alternator) is showing them to be charged, then I'm thinking the alternator has to be bad.
It could be that the higher alternator reading we had earlier were from bad batteries in the meters because we ended up changing batteries in both after some odd readings.
So. I'm going to install the new alternator because I have run out of time and choices. Gary