USB requirements are rather stringent. Unless
the 12 MHz crystal has changed radically in frequency, it should
be pretty much left alone. (If it has changed or if it interferes,
the best solution is to replace the whole thing). Easy enough to determine:
try using the USB interface. If it communicates, all is ok.
Usually in the arduino, as in most uC's, most RFI problems are traced to the
external (16 MHz) crystal, or leakage into the power supply. If one is
not ready to replace the unit, the best solution is a new crystal; it can be
any of a number of frequencies. What changes is the timing span.
Alternately, one can try to shield everything -- especially the leads
going to other parts of the rig. Sometimes, the lcd is noisy and not
much can be done about it except to change the programming to
change the update method. But usually, that is a KHz and
not a MHz problem. In this case I would not discount it, however,
since the problem is audio sidebands.