Thank you for the great documentation of your investigations.
You should have seen a 2-3x reduction in noise in the 100-1000 second range with the ADA4522 chopper opamp.
I use one of my Z10 prototype Voltage Standards when I do the 10V stability test. It has shown 3nV stability over a day when Air pressure and Linear drift affects are removed.
I could only get good Zero stability results by using a simple copper wire short or a gold-plated PCB shorting the input terminals. One shorting plug with gold plated banana jacks had noticeably higher thermal emf and Zero instability.
I have modified 3 units now with good results. There are a few other subtle things I do when modifying the units. I have not quantified these improvements. We are dealing with nanovolt stability over hours.
To minimize noise from thermal EMF, I minimize the A1 shielded enclosure airflow. I close off any openings at the aft end, near the fan, with tape. There are a few holes back there and there are gaps where wiring leaves the plastic shield around the power supply area. I have not noticed a change in compartment temperature by doing this.
On the A3 module I use small cotton balls around the +-12v Opamp and the first comparator. This minimizes any random airflow in this area especially with the DIP to SOIC adapters needed for the newer opamp. On one unit I put cotton balls on the back side of the pcb to also cover the pcb pins and the U180 pins. I pull the cotton balls apart to fluff them up a little.
Do not block the cooling of the EL2018 comparators. They already run hot as it is.
All the pcb mounting screws on A1 and A3 modules need to be tight. Do not break anything but they need to be snug with no missing screws. I expect HP to have a torque spec for these screws somewhere. These screws supply critical grounding for the HP3458A pcbs. Screws made from different metal are not allowed.
With chopper Opamps I add a C0G capacitor between the non-inverting input to chip power ground. I do this on the SOIC adapter pcb. This will minimize current spikes getting into the circuitry.
The parts list for the A3 module specifies 10nF AVX X7R capacitors (AVX PN SA101C…) for the opamp feedback. An X7R capacitor can have 10x the current noise of a good C0G cap. These are C160, C165, C151 and C152. I have removed some of these capacitors by clipping them off the pcb and testing them. Based on leakage current noise they appear to be C0G caps. HP made several different A3 versions over the years. I cannot guarantee what type of capacitor is on your PCB. I replaced the critical 10nf feedback caps with TDK 10nf 100V C0G parts so I know I have the best.
NOTE: If you want to test an X7R capacitor do not unsolder it from the pcb, clip it out. The Heat from unsoldering may change the X7R capacitor characteristics like aging and leakage current.
As I am sure you know, there are several better chopper Opamp than the ADA4522. Below 0.1 Hz the ADA4522 voltage noise density starts to rise like a normal opamp. It still should have 10x less noise than a Bipolar LT1001 opamp at the longer time scales (100-1000 seconds).
The ADA4523, OPA182 and the OPA189 have flat noise spectrums out to 1000 seconds.
On the A3 module I have successfully tested the -
OPA210 Super Beta 2nV Bipolar Opamp, 5x less noise than the LT1001 and lower bias current.
OPA182 5nV chopper (low power OPA189), OPA189 5nV chopper, ADA4523 4nV chopper.
I not have noticed any strange operation over the last year from chopper clock noise interacting with the A3 sampling frequency.
I have also tested the choppers and the Super Beta Opamp in the U110 First comparator location with no noticeable issues.
I changed the U170 opamp (DCBUF) from an LM358 to a OPA2140 for much better bias current stability (1000x), faster operation (faster settling, lower output Z), and better DC specifications.
Good luck!