If I'm just using the usb input does that avoid jitter issues and the necessity of a higher quality pc?
The USB input uses IC's as clock generators (as far as I understand will look in to it more), that is not ideal, you want dual high precision crystal oscillators for that.
More stable clock = less jitter.
But for a stable clock, the USB transport (or USB input section) needs a stable power supply as well.
But the USB input on the Yamaha is proprietary, you may need to use it for DSD playback from a computer, but I just don't know.
The USB input only cares about two things, maybe three
1. The PC needs USB 2.0 or higher.
2. The PC needs sufficiently low DPC latency to avoid pops and clicks in the sound.
3. The USB input MAY be powered by the USB bus in the computer, we can't know for sure without testing it, using a USB cable that doesn't carry power.
If the USB input doesn't work without USB power, then it is USB powered.
If it is indeed USB powered, it will struggle with dirty power form the computer, this can be solved with a USB power supply, a AQVOX low noise USB PSU fx.
This affects ALL computers, unless some special audio grade USB controller is added (PCI/PCI-E card).
I think I remembered it all.
Edit: no I don't see any crystal oscillators in the CD-S3000.