wow, the 1000 SM schematic is different than what you have for that model. It labels that 12AU7 pot VR9, and step 5 of the MPX alignment has one use it to do the standard separation adjustment - play a tone on one channel, use the VR9 50k pot to minimize the other channel. I got my 1000 SM and schematic at hifiengine. They have the 1000A too
Step 5 calls it "VR", but it's the only pot available on the top deck in the MPX area, clearly labeled in the SM picture.
I would clean the tube pins, and swap in another tube at this point. It's very likely the pot is bad otherwise. It's 50k, so swapping in two equal value resistors close to 25k each would let you replace the pot for diagnostics. Or use a 50k pot laying around there.
Also note the SM1000 MPX has different 12AU7 resistor values from cathode to gnd - 15K versus 50K.
Was this a fix? With the same 20k plate resistors, changing It should bias the tube to idle with more current, but also likely gives the separation more adjustment range. Check the two 12au7 grid to gnd voltages. These DC values should change as you adjust the pot back and forth, going up one way, and down rotating the other way.
I would also replace those 10M resistors with low noise drift free units. They could be flaky, too no matter how they test. One could be drifting like crazy with elevated temps.