With the LM311 for the 50 Hz signal there should be no ringing at the output. The supply should have isolating resistors if needed. At least the extra signal would be mains synchronous and thus suppressed quite well.
The PLL should definitely have a clean supply.
I saw ringing at the output on both the rise and fall of the square wave, and some noise on the ZC at the input.
Just checked again and it's quiet. I think I screen captured the earlier ringing. If I can locate the captured images I'll post them.
I experimented with isolating the PLL supply and lowering the voltage. With the I2C lines from the 18F252 now being higher they introduce significant noise to PLL as pulses on the supply. Is it OK inserted resistors into the I2C lines to mitigate this? Not sure I want to lower the supply to the timing PIC.
The can for the µC is a little odd - there are plenty other µCs and possibly EMI sources in the DMM. Also with no realy filtering in the supply the cans are not very tight. As far as I can see the PLL was outside the cans. So chances are the can around the µCs is not really needed. Improved decoupling / supply filtering is likely more effective.
The can around the integrator has a dual effect. One is a little EMI reduction - again without porper filtering the supply not very effective. The other is to improve thermal stability for the integrator and switches. I still don't think the can is really needed. With an AZ OP the integrator would not be that sensitive. The more sensitive part would be the reference amplification.
I have my suspicions that the cans on the ADC has a lot to do with obfuscation.
I'll experiment and see what effect running without cans has.
The most significant EMI output is directly under the ADC PCB. The 10MHz clock that is used to output a PPS trigger for the main micro.
The oscillator itself isn't that bad, but on my revision the supply resistor (R119 10R) is cut and a pair of wires tun to a internal/external 10MHz switch. These wires hoot quite a signal. I'm thinking of switching the oscillator supply with a FET rather than have the supply running to the switch and back.
It's a same the 10MHz is on the unguarded size of DMM. It could be used to clock everything on the ADC otherwise.
For many parts I see no real advantages with THT parts. SMD resistors are much easier to exchange if needed. 0805 size are still reasonable readable and easy to solder. The film capacitors kind of need to be THT. Combined THT and SMD can be a bit tricky: the THT parts can block the access to soldering the SMD parts. So it helps if the SMD parts are on the bottom.
Mounting the SMD parts on the underside of this PCB isn't something I'd considered. I'll bear it in mind though whilst I'm laying it out.