I've never touched a -12, so, having said that...
If the noise goes away when the intercom is switched to Pilot Isolate, then it's unlikely that the alternator/regulator is really the culprit. Shielding is unlikely to help much, if at all. I'd look at the areas that are getting isolated. In other words, the copilot mic/headset wiring, any aux inputs, etc. And if the plans don't show keeping all the audio ground runs isolated from the airframe, well, they're aircraft designers.
Herding electrons is a completely different discipline. Find the intercom's installation manual, and the radios' install manuals, and follow them as closely as possible. They will likely show shields on everything; nothing wrong with that, but it's really prophylactic more than required. The reason is that the audio paths are such low impedance (<600 ohms) that it's really difficult for RF energy to get radiated into the wires. The big thing to watch is how the grounds are handled, because that's likely where your noise is getting injected.
I *think* that the stock alternator on a 912 is a 'dynamo' permanent magnet style which would mean that there's raw AC coming out of the alternator (not a big deal), and the 'regulator' is actually the diode block plus the regulator in the same package. If you're going to do any filtering of the alternator, it would be on the DC wire that comes out of the 'regulator' block and feeds 14V to the aircraft.