@filipm R16 could have been sacrificed due to a bad tube - which can happen in any tube gear - if that was the case be happy that was the only thing that died.
But - dpop and audiophile1 are correct - this is more of a puzzle than searching for that best sound. The EAR has quite the reputation, but if you just want fantastic sound and not this hassle, you might want to consider an alternate route.
For me, it’s both as I love a good puzzle and great sound. I will add that is seems to be similar for a lot of the folks over at audiokarma dot org - they have quite a few posts on building EAR clones over there, and so far us audiogoner’s here have not been able to solve this. They helped me through a number of puzzles in the past.
Back to your problem. It’s possible you have a combination of a power issue in your place and the EAR is not dealing well with it, potentially due to near failing components. If power is the issue the power company must fix it. But if they cannot, I’ve no personal experience on what you need to do. I would research double-conversion power units - (AC to DC to AC) with a complete separation from the AC power; I believe there some out there are running their audio completely on these things, but I think it has to be complete - no component can be plugged into the wall or your risk a ground loop issue again - so big and expensive. Make sure you can return it if it does not work for you.
On the EAR, given that you had to replace some parts already, best to replace all those electrolytic capacitors as well. I think the EAR came out in the late 90’s, and if this is an original unit, those electrolytic’s in the power supply especially may be near end of life. They are cheap and easy to replace. Just make sure to find units with the same capacitance with same voltage rating or higher and similar dimensions. Nichicon, United Chemicon 105+C caps would be good for the power supply. I would also while you are there reflow all the solder joints on the boards. Takes less time than you think, and that way you are assured there are no bad joints.
When you replaced those film capacitors, did you use new ones of the same capacitance and voltage? The voltage could be higher, but I believe the capacitance value needs to be exact or near exact or it could negatively affect the circuit. For R16, - same - did you use the exact same resistance and wattage value? I think higher wattage would be ok though, especially if the old one burned out for an unknown reason.
One other thing - I noticed the step-up transformers in your EAR - does pressing the MC/MM switch have any effect on the noise with the shorting plugs on? If so that may be your ground issue there - reflow the solder!