Another update:
* I added the LT5400-6 for the +12 Sum as other boards have used. I'm presuming that the slightly different ratio, leading to a slightly different sum vs. the genuine U180, is acceptable given the hoped-for better TCR tracking. A question: is there any reason that the left-over LT5400-1 resistors are floating, as seen in some other boards? I've grounded them.
* More tuning of traces, etc. I still haven't removed the ground fill around the serpentine traces, and may not in the end.
So now, other than any further noise suppression, it's about finished.
* For lower noise, I suggest moving to 2.7V logic for the inverter and FF. The switches will be within spec at that voltage. The inverter I specified in V0.4 was the SN74LVC1GU04, which can operate with up to 5.5V inputs at 2.7V supply voltage, so it remains OK. The FF would need to change, perhaps to the SN54LCTH574, which can operate at 2.7V with up to 5.5V inputs as well (i.e., 2.7V from the inverter and ~4V from the CPLD). The regulators would change too, naturally.
* Using a high PSSR, LDO regulator on Vdd2, e.g. from 4.4V to say 4V, may help, and I think we can afford that modest drop in voltage. It's a pity that we can't conveniently do the same for GND2. Opinions?
* Wanghar added ferrite beads, both globally and locally, in a few cases. I'm a little leery of those due to the possibility that they may actually increase ringing, but a Pi network at the supply inputs (vs. just a large ceramic) is somewhat common and might be helpful. E.g. 47 uF Tantalum -> 10 Ohm ferrite bead -> 22 uF X7R ceramic for global power inputs.
Locally for the FF and inverter, I am already using high PSSR, LDO regulators, with additional 10 and 0.1 uF capacitors. That is probably sufficient, and I'm unsure if adding ferrite beads would help any further.
For the CPLD, which is likely to be a source of noise, I suppose adding additional local bulk capacitance might help (e.g. additional local 1 and/or 10 uF ceramics). The space is tight between signal traces, but the bulk caps probably don't need to be super close to the power pins. I don't know if ferrites would help, and wanghar did not add any here.
What else could be done? I'm not an expert on the topic of noise suppression, so please offer opinions about any of the above.
Thanks.