However, I'm now considering an MCU based design to discipline my rubidium frequency reference to eliminate dielectric absorption issues in long time constant analogue LPFs, hence my interest in this topic thread which raised the issue of significant diurnal phase shifts in the GPS time pulses.
Can there really be as much as 30 to 50ns diurnal variation?
Yes. I don't remember the exact numbers but you can expect such drifts over a 24 hour period from a GPSDO. I have done some testing between GPSDOs and a Cesium clock that show drifts in the tens of ns over a 48 hour period. I don't know the URL but it is possible to get data that provides you with the GPS time offsets that tell you the error in your GPS receiver. If you combine these with the adjustments you did in the oscillator, you can characterise your oscillator and with enough data, you might be able to do pre-emptive adjustments or use longer time averaging time intervals. This all depends on the stability of the oscillator but based on worst case specs even a Rb oscillator is likely to drift more than several tens of ns in 24 hours.
Many thanks for that swift response.

Oddly enough, shortly after posting my question, I noticed a reversal of today's ~1ns/hour downward drift of the ruby versus my 'Simple GPSDO' just minutes after local sunset. I rather think I'd just observed the beginnings of this diurnal phase shift effect just where one might expect it to come into play at the day/night transition periods of this daily cycle.
Another factor that reinforces this observation being the fact that overnight test runs generally displayed the least drift and disciplining wobble, exactly the time period when the ionosphere in the unlit hemisphere could be expected to be at its least dense and most stable condition.
With regard to stability of Rb oscillators, most home lab concoctions (the Rb frequency reference projects described in you tube videos at any rate) would be doing extremely well to achieve daily phase shift rates below 100ns unless they happened to fortuitously be one of the few examples exhibiting an extremely low tempco by pure blind chance alone to start with.
Just throwing a Rb oscillator into an enclosure designed one way or another merely to prevent overheating (or not in some cases!) is no way to create a stable home lab RFS imo, hence my now two year old project to do my LPRO 101 the justice it deserves.
I started off with a simple analogue on/off thermostatic fan controller which, whilst it did improve the ruby's stability, offered no cost effective option to include barometric compensation, so a few months of experimentation later, I took the plunge into programming an Arduino Nano to the task, never once regretting this change of strategy ever since.
It's that experience which now has me turning away from the G3RUH 'Simple GPSDO' option, as fine as it was, and finally taking a serious look at the MCU control option in my next GPSDO/GPSDRO project. I'm going to start with a GPSDRO simply because I should be able to bypass the horrendously destabilising tempco issues that seemed to have plagued a lot of the DIY mcu gpsdo designs that had been described in various EEVBlog topic threads.
I can thermally bond any temperature critical components (including resistors) onto the thermally stabilised heat spreader to 'cheat my way past' any such tempco issues, maximising the return on all the effort I'd invested over the past two years on achieving a constant 36.10 degree (+/- 30mK or so) base plate temperature.
Now that I'm aware of this diurnal phase shift issue with the GPS timing pulses, I can lay my RFS project to rest until I can at least create a more stable gpsdo reference. I also have a Symmetricom SA.22C awaiting a similar improvement exercise so I think the sequence will be:-
Convert the LPRO into a GPSDRO to use as my reference standard to calibrate the Symmetricom SA.22C based RFS to convert that into a second GPSDRO which can then be used to finish refining the stand alone performance of the LPRO by a radical revamp of the insulation and cooling pathways with an exhaust gallery to allow servo controlled valves to gradually transition from full through flow to fully recirculated exhaust back to the intake plenum to ease speed control demands on the cooling fan to provide finer temperature control over a much extended ambient range (from a 33 deg max, down to quite possibly even sub zero ambient temperatures!).
The current limits are 32 deg max down to around a 15 deg minimum before the controller is obliged to stop the fan and resort to on/off control. The problem in this case being the need to give a starting 'kick' to un-stick a brushless DC fan without over-cooling the heatsink under such cool air intake conditions. Even then, this low operating temp limit was only achieved by placing a damper in the intake vent, hence the 1 degree sacrifice on the max ambient temperature margin.
I've attached a photo of the LPRO based RFS along with a screenshot showing the drift since 1 minute past midnight to 22:00 this evening. The trace had started at the LHS, reached the RHS around sunset just over 16 hours later before sweeping leftwards to its current location where it seems to have stood still for the past hour.
You can see the 'scope in the background of the photo along with that of the SDM3065X displaying the current lamp voltage supplied from the lower of the two stereo jacks which also provides access to the XTal voltage. The upper jack socket provides access to the 5v reference at the hot end of the cal pot and that of its wiper contact which is linked to the 'C Field' pin via a (temperature stabilised) 3 Mohm resistor. That RFS box, btw, is 12 inches wide by 8 inches tall by 10 inches deep! It needs to be that big simply to accommodate all the insulation and ventilation galleries.
[EDIT 2022-11-20]
I've added a new photo. Can you spot the difference?
