First, a quick note on the PZT I thought I killed- it was most likely something in the high voltage amplifier that broke, since I put the amplifier in another STACIS with a working y-axis PZT and it still didn't work properly. Conclusion: something in the y-axis amplifier circuitry is broken, not the PZT itself.
Today I retook the open loop gains in the X and Z axes (Y axis out of commission for now, see above). With the loop open, I input a swept sine signal from 0.1 to 100 Hz, and measure the output of the geophones. This way all the transfer function that are present in the closed loop are present here as well: the transfer functions of the physical STACIS, the geophone pre-amplifier circuit, the high-voltage amplifier, and the PZT actuators.
Here is a block diagram showing what I am measuring, with the various transfer functions in blue boxes (the measurement is their product):
These open loop gains show there is gain of at least 10x from 2 to 80 Hz in the z-axis and 2 to 60 Hz in the x-axis. This is the region I was seeing isolation in when I switched to closed loop, which is consistent. These measurements were with all the pots in the geophone preamplifier set very low, so more gain (and thus isolation) is hypothetically possible if I find a way to stop the horizontal axes from becoming unstable at higher gains. There is unity gain at around 0.5 Hz and 100 Hz for the z-axis, but the phase is nowhere near 180 deg. at these points so there shouldn't be instability due to this. The peak at around 15 Hz is consistent with old records of the STACIS open loop gain.