Ok, so here's the outcome.
The dealer put the rebuilt alternator back. It's running fine, probably better than when I got it a few months ago. Note, originally there was a rattling sound that indicated a bad pulley. Similar to what was experience by the fellow who posted this topic:
Lost my idler pulley Fri.
So the combination of a bad pulley and a worn rotor in the alternator caused a variety of "bad engine noises": a low frequency rumble/rattle at low rpms and a sound that I had originally thought was a gearbox whine around 3000rpm.
All the noises are now gone and the engine sounds very smooth again.
I advise people to listen carefully to the sound their engine makes. If you hear an abnormal rattle or low frequency rumble then it might very well be a pulley(s) and/or the a worn rotor in the alternator. Get it serviced as soon as you can. I noticed in mine that once the wear in either the pulley or the alternator (or both) manifests itself, it gets worse quickly.
If it turns out that it's a worn rotor in the alternator, you may want to consider doing what I did, namely: have the alternator rebuilt by a specialty shop for about $150 USD instead of paying $1100 for an OEM Porsche alternator. Only time will tell how well the rebuild went, but the new pulleys and re-worked rotor in the alternator returned my Boxster engine to the sweet sounding beauty it was before.
Hybrid Mode
