Check and/or replace the headshell wires.
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Sorry to hear about your issue. I also own the Proteus, which surely is a great cartridge. To be honest this doesn't really sound like a cartridge problem. I'm also pretty sure it has nothing to do with anti-skating, azimuth ot other alignment related issues.
So I guess you should try to be as methodical as possible. First you might consider trying the Proteus in a different system. I suspect this will rule out the cartridge as the culprit. Your description more likely suggests a cable issue. A loose contact perhaps, either with the tonearm inside cabling or the tonearm cable to the phono amp.
You need to systematically determine where the problem lies, and not assume it is the cartridge. Because you think it is the cartridge, start at that end. Switch the left and right wiring of the wires at the pins of the cartridge. If the problem changes sides, then it is the cartridge that is causing the problem. If it doesn't switch sides, the problem is somewhere downstream of the cartridge (tonearm wiring, interconnect to phono stage, etc.). You can work backwards switching left and right.to isolate the source of your problem. Intermittent fading or loss of signal is often a problem with an interconnect or a problem at the jack where the inteconnect feeds into.
I just saw that you switched cartridges and the problem is the Transfiguration. The builder died not too long ago, and, I believe, production has stopped so there might not be a way to get Transfiguration to check on your problem. Rebuilders/re-tippers would be able to do something if the problem is with the stylus, but, it sounds like a problem with the wiring (winding of the coil) and that might not be repairable.
You might want to talk to Bob Clarke at Profundo; he is or was the U.S> distributor of Transfiguration.
Yes I think an autopsy is a good idea.
Bear in mind that if you apply a soldering iron to make sure no residual solder actually makes contact. (Gold can/will diffuse into solder although that comment applies to old-fashioned tin/lead.)
My first thought was to suspect the coil/s but I would have expected a complete O/C rather than intermittent signal. As a matter of interest does your captive tonearm cable terminate at the base of the tonearm or continue all the way to the pre-amp?
That is a bit of a scary option. If there is an open circuit because of a bad solder connection of the wires from the coil to the pin, that might cure the problem. But, if you apply heat too long (something pretty hard to judge) you might cause all kinds of additional damage.
I would NOT do this myself until the cartridge has been sent to an expert for examination. If you get it back with the word that it is junk, then maybe it is worth a try. BUT NEVER before.
Send it to SoundSmith or others that do this kind of work.