Hey, I think you need to approach debugging this a little differently!
First of all, grab (or borrow) a regular electric guitar with passive pickups. Plug that into your Blues Deluxe and see whether you can get a suitably loud clean sound (well, you should be able to get a ridiculously loud clean tone!). If you can't get a clean tone with a Strat, then there's something wrong with the amp. You would need to debug that starting with a known good 12AX7 preamp tube which you sub in with the current preamp tubes to find the bad one. Power tubes are more likely to fail in a guitar amp (they work harder), but less likely to fail the way you describe.
If you can get a loud clean tone with a passive guitar, then mark down the knob settings that you got the good tone with. The active electronics in your Alembic can generate much higher output levels than a passive guitar, so your problem may be that the output of the guitar is overdriving the amp inputs. So, what you want to do now is to try matching the output level of your Alembic to roughly the level of the passive. It doesn't need to match dead on, but you want to try to get in the same ballpark.
If you're a highly disciplined guy, you can do this with the guitar plugged in and the amp turned up. But for most people, you're much better off unplugging the guitar, setting the guitar's internal gain pot midway, then plugging it in and seeing whether it seems louder or softer. Unplug, and adjust the pot a little, the plug back in and test again, flipping back to the other guitar if you need to get a reference. The reason you want to do this unplugged is that if you slip off that tiny trimpot and touch anything else in the cavity you can deliver an amp-killing thump at the guitar's output, which you really don't want to do.
Once you've matched the output level of the guitars, see whether you're having the distortion problem anymore. Different guitars just sound different - one may be bassy, another trebly - which will influence the output and overdrive of the amp. This may lead you to tweak a bit more.
If you're at a point where the passive guitar sounds good (good tone and good volume) and your Alembic is still sounding distorted in a way that's not related to the tone, then there's probably something wrong with the internal electronics on the Alembic.
From your description, it sounds like it's likely to be the internal gain adjustment. It was too high when you started which overloaded the amp input, then, when you turned it down all the way, it was too low, which is why you couldn't get any output level from the amp. If you adjust the Alembic to be at the same output level, then you'll be comparing the tone of the two guitars.
Hope this helps,
David Fung
