Electronic – Shielding and Ground Loops – RF panel jacks for GPS

I think you're on the right path, a couple of notes,

1) With a signal trace between two planes, the return current will split between the two planes, even if one of the planes is split. The return current cannot "see the future" and decide ahead of time which plane to return on. It will return above and below the trace until it sees the split at which point is says "oh crap!" and pays you back by possibly causing you to fail FCC testing. So you want to avoid running traces over plane splits even if another adjacent plane is not split. You can deal with splits with capacitors and such but this type of solution is less than ideal. I'd focus on always avoiding running a trace over a plane split on an adjacent plane.

2) Wide return paths on DC signals don't really matter.

3) You asked about two signal layers sharing the same plane. Usually, this is not a big deal if done properly. What many people do is use one of the layers as a "horizontal" signal layer and the other as a "vertical" signal layer so the return currents are orthogonal to each other. It is very common to route two signal layers for each plane, and use this horizontal/vertical technique. The most important thing to remember is to not change reference planes. Your setup could be a little tricky because going from the bottom layer to the 4th layer adds another return plane. More typical 6 layer boards are

1)ASignalHor 2)GND 3)ASignalVer 4)BSignalHor 5)POWER 6)BSignalVer

If you need smaller additional planes, like under the micro, these would usually be placed as an island on one of the signal layers. If you need to use more power planes, you might want to think about going to 10+ layers.

4) Plane spacing is important, and can have huge impact on performance, so you should specify this to the board house. If you take the example 6 layer stackup I mentioned above, spacing of .005 .005 .040 .005 .005 (instead of standard stackup with equal distance between layers) can make an order of magnitude improvement. It keeps the signal layers close to their reference plane (smaller loops).

Yes, it sounds like (a little confusing) you have a ground loop problem, and yes they can matter, especially when trying to measure small analog signals. If all grounds tie back to the same outlet strip via relatively short line cords, then it would probably be OK. However, you say that this cryostat thing (whatever that is) is connected separately to building ground, so that is obviously not the case and it's confusing therefore why you brought it up.

In general, it's good to convert analog signals to digital as close as possible to the source, then ship around digital signals. Those are much easier to isolate, like via opto-couplers, pulse transformers, radio, etc. In other words, a old fashioned A/D card in the computer is not the best overall architecture from a system level point of view.

However, look at the A/D card carefully. Most likely it can be configured for single ended and differential operation. This is a case where you want differential inputs. The cryostat thingy may produce a ground referenced signal, but take its ground and output signal as being differential. This will essentially subtract the ground offset from the signal before converting it.

This trick will only work up to some frequency, probably a few kHz or low 10s of kHz. It should work pretty well in subtracting off any ground signal due to 60 Hz or 50 Hz power line return currents accross ground paths in the loop. Sharp common mode spikes can still confuse the diff amp in the A/D and show up as noise in the final output. It's worth a try though. If it's not good enough, go back and convert to digital at the sensor, then opto-isolate the digital telemetry signal.