You can grab iron ferrite chokes from old power supplies. I usually find them there and in other old equipment.
I usually accepted noise as a trade-off with the Shuttle since it's so densely packed and the PSU is not very well shielded and right above all your outputs.
Find a way to use your coax or optical SPDIF on that computer?
You can get humbuckers for audio lines? I thought they were just in my pickups