[DaveWM]

ok so now we know for sure the HV is working and can focus on the regulator circuit.

you need to connect the anode lead back up on the regulator, then get some leads to the cathode and grid for the shunt tube. check the voltages of those leads compare to the sams.

There is not much to go wrong with a CTC-12 regulator. I would suspect the pot but you said it was tested and (you actually tested the pot with a meter for resistance and wiper function). the 2 resistors are fairly close, that leaves the .0033 cap from cathode to grid. if it was leaky at all it would upset the shunt bias.
Note the cap is a disc cap and not likely to be bad, but its pretty much the only thing left to check.


OR you have a gassy shunt tube. do you see any purple glowing from the shunt tube?