Great design, great board, great build!   
 
The tone controls are different from the standard Fender/Marshall tone stack.  First and foremost, the tone controls do not interact like they do in the Fender/Marshall tone stack. The BASS control works like the Bass control on the Timmy or the Tight control on a Thermionic.  The MID is an active cut/boost.  The TREBLE control is a bass/treble balance control much like a BMP Tone control or the Fender/Marshall Treble control.
Did you have an issue dialing in the JFET bias?  What is the drain voltage?