Here are some Super Axe pictures and schematics I have collected in past years. Unfortunately, some are such low resolution that they have to be interpreted with a bit of imagination.
I have not had a Super Axe guitar, so I'm guessing at what some of this is.
The controls:
Separate from the control panel there is a single pickup switch. No pickup volume controls.
Controls in the control panel:
The modules. Control panel and two black box modules.
The larger black box module seems to be the phaser, the smaller black box module seems to be the compressor.
Control panel sketch:
Inside the phaser module:
Schematic including pickups and pickup switch (or switches)
It seems to show some complex switching of the pickups, perhaps phase reversal switching.
Most of that witching seems not to be present in the single pickup switch models.
The schematic is hard to read. It says FRONT PICKUP and BACK PICKUP at the left side.
Schematic omitting the pickups:
Schematic of phaser:
Schematic of compressor:
As to what is making the tone very dark and bassy, I'm not sure. Here are a few things to try.
It appears the two modules have plugs on them. If so, Unplug one at a time, carefully. Suggest the compressor first. The pickups go to the compressor all the time, even when the compressor switch is set to off. and it something in it is loading down the tone, then unplugging that module may let the rest work. Perhaps its input section has a problem and is letting its input capacitor act as a tone capacitor loading down the treble. If there are no plugs on the modules, then you may have to disconnect the wire to the input of the compressor module.
The tone control is near the output. The tone control pot has three terminals. Two are connected together. If somehow the third terminal of the tone control pot has become shorted (connected) to the other two terminals, or to ground, then it will be like the tone control is turned for minimum treble all the time.
If none of that works, you may need to disconnect the wire from the pickup switch where it goes into the control panel, and temporarily connect it straight to an amplifier, bypassing all the electronics in the Super Axe. That will give a test of whether the problem is in the pickups (if the tone is still dark and bassy) or in the Super Axe electronics.
...Richard