Usual answer for noise in low power signals is cooling.
So wrap the crystals in a cooling jacket.
Simple answer is a closed loop with anti freeze, being good down to a few 10s of degrees below C.
Beyond that you're into LO2, LN2, LH2 and LHe, with progressive levels of nastiness.
Thumbs up for the enormous enlargement but the computing procedure sounds more like the days of analog computing, when programmers re-configured the wiring between op-amp modules to change what was being computed. Keep in mind that tech was how the early flight simulators could give real time response to control inputs when the digital hardware of the day would take seconds to solve the equivalent equations and drive the actuators.