I'd first change the 10uF electro coupling cap (C7 on the Harley Benton Ultimate Drive schematic - I believe it's C9 on the Joyo PCB) to around 0.1uF in film. This will remove a lot of the boominess.

So, here's a newbie question: if the polarized capacitors are facing the wrong direction in the circuit, how is the circuit even working? I've been researching electronics recently, and I thought that might stop the signal entirely, like a diode facing the wrong direction. In fact, I saw a tutorial...

Apparently the polarity of those two 10mf coupling caps are reversed (on purpose?) on Fulltone's Ultimate Overdrive, and the Joyo appears to be an exact clone of that, not of the Foxx Tone Machine. Those 47n and 100n caps are also switched on the two. I'm going to wire my Joyo both ways and see what...