Probably not it, but I wonder if there might be problems with setup/hold times on the flip flops. If the uC output toggles too close to the clock edge the flip-flop may do odd stuff
As noted before the setup time for the flipflop should be OK: some 45 ns setup and some 15 ns hold time. 74HC74 calls for a minimum of 15 ns setup and 3 ns hold time. So this looks good, like a near perfect phase setting.
I have not checked with the extra resistor. The resistor is expected to delay the clock to the µC and would thus reduce the setup time and increase the hold time. Getting too close to the limit may let some jitter through even if inside the set-up specs. A slightly lower clock may help - something like 8-10 MHz clock should be OK for the rest.
How the clock is effected is still not clear. I have 3 main suspects: one is capacitive coupling directly to the clock output pin of the oscillator and this may upset the actual oscillator inside. So the upset may cause some frequency modulation.
A 2nd possible way could be the internal state of the µC effecting the input capacitance of the clock pin and this way effecting the load to the oscillator. This may effect the frequency and the delay to the µC. I was hoping the 68 ohms resistor would reduce this effect, but the 68 Ohms are probably to low and the additional damping could be just as bad.
The ground path may introduce transient shifts for the µC and this way effect the load from the µC - however this would be more short time.
So for a new board an extra buffer is definitely a good idea.
The circuit has not really changes much in the last year or so: I went one small step back at the slope amplifier, using diodes only and no longer the transistor as a diode substitute. With the transistor there was quite some drift in the DC level, so the ADC needed some 30 minutes of warm up before working. This was probably from to much reverse recovery with only the BE junction. It may get better with the collector connected to the base, but I have not tested yet. The diode is also not perfect - it shows a little more drift in the gain for the µC internal gain.
I think I would skip in the option to use the scaled down main reference for the µC internal ADC: The gain of the slope amplifier is not that stable anyway and the supply as reference is good enough.
For the resistors the ORN or MORN resistor array seem to be the best bet now, as they offer 50 K with low noise (comparable to LT5400) - I have not tested (only ordered), but they should work OK. The TC matching may differ, but chances are good to get good enough matching.
I have tested the already optional ground buffer OP - it works about as good as with the direct ground. The difference is that with the ground buffer one can better use an external reference module as there would be very little load to the reference ground. Some of the candidate OPs for the integrator are available in duals - some, like OPA1678 even as duals only. A dual OP makes sense, as the current is switched between the 2 OP outputs.
A point may be reducing the µC voltage to some 3.3 V, as the modern crystal oscillators are often only some 3.6 V max.. This would not change much with the board: The 74LV4053 switch would change to a LVT4053 and get a separate regulation - just like in the 34401.