Wow... Sadly, this is not an uncommon tale of a person buying one of these that has been mistreated in the past.
I was actually out in the Bay Area a few months ago, and could certainly work up a plan to go back, but I think we need a plan of action first.
Can you record a video of the engine idling both when cold and again when warmed up and making these noises you want to point out? Please do it from the center of the bumper aiming at the engine - but stand at least 1 step back from the bumper so that the wind from the fan doesn't cause rumble in the microphone. I'm specifically interested in the sound of the engine.
You can email them to me or post a link here, to the file in your Dropbox Public Folder. If you don't have Dropbox, you can use this link to sign up for free and we both get bonus space:
https://db.tt/QGC2eH5GWhen you sign up and install the program, it will create a special synchronized folder on your computer. One of them is called "Public" and any file in it has a special link (found when right-clicking on the file) that you can copy and paste in forums like this. (Fun tip: This is the easiest way to post images too)
Anyway, hopefully the damage is not as bad as you think. In my experience, as long as the CRD is able to move under its own power for any decent length of time, everything else is fixable. These things don't put up with problems for very long OR very politely.