remove the shield of the usb cable.
only let red (5V), black( GND), white and green (data) go to the board.
the at least the ground-loop is cut off.
ferrite bead: perhaps you have a old mainboard lay around?
600khz buk reg: do you have mounted both asic bukregs? but only use 1 for the asics and the other one is "idle"
The 5V is n/c anyway.
Good idea on mainboard - I do have an old ASUS P4 board here I can hack up. I'll check that out today. Right now I have to go into town for something, so it'll be a few hours.
Both buck regs are mounted but only one side is used. You're thinking the unused one, not under load is putting out RFI to the other. I'll be adding more chips to the 2nd bank soon. The 600kHz noise isn't much anyway - just small blips compared to the noise I was getting from USB.