If the fault, affecting the disc input only, is in the amplifier and not in the cartridge or its connections, then it would appear to be in either the disc adaptor board, the preamplifier board or perhaps the input switching. Most of the equalization components are on the disc adaptor board, and are shared between the M1 and M2 positions. My understanding – from the board diagram - is that they swap channels between the M1 and M2 positions of the board. So a fault in the M1/M2-specific circuitry on this board that appears in one channel only at the M1 position should appear in the other channel at the M2 position.
If it the fault doesn’t move with the M1-to-M2 swap, then it probably lies in the preamplifier board, or in the input switching just downstream of that board. As an additional check, perhaps fed a “line” source into the disc input with the board at the C1 position. It will sound odd (bass boost) but should show up any channel differences whose cause lies not in the M1/M2 equalizing circuitry.
Here is a simplified version of the Quad 33 disc input amplifier, positions M1 and M2, taken from P.J. Baxandall’s writings, showing commonality of most components, although not showing the channel swap:
And for completeness, derivatives of that for the C1 and S positions of the disc adaptor board:
Cheers,