Have you taken this into consideration:
From
alembic.com, Plugging into Jack 1 alone gives full sensitivity, while Jack 2 alone is attenuated 6 dB. If signals are plugged into both jacks simultaneously, mixing resistors combine the signals
If I recall correctly, with two signals plugged into channel 2, each will be attenuated 3dB.
I'm guessing your intent is that B will be cleaner, while A will be more overdriven. And I'm guessing that by experimenting with jack choice and volume setting on channel 1, you should be able to get the volume outputs of A and B matched.
And from the same page, The signal from Channel A is high enough to drive the first stage of Channel B into distortion. The tone controls of Channel A are used to emphasize those frequencies which will be most distorted, while the controls of Channel B shape the color of the resulting distortion. Channel A's volume control sets the amount of distortion, while the Volume Control of Channel B sets the output level (Master Volume).
Here, your channel 2 tone controls will be first used to shape the tone of B, but will also affect what is flowing from A. But here again, with experimentation of the tone settings on channel 1, it seems that a useful result can be obtained.