Using LTSPICE, I modeled the Two-Rock John Mayer Signature to understand more about the circuit. LTSPICE makes it easy to change resistor/capacitor values and see a graph of the signal throughout the circuit. It was a bit of a learning curve as I've never had simulated circuits in such detail like this. I borrowed some bits and pieces of open source LTSPICE models around the internet to pull it all together.
One thing I noticed while researching the JM Sig circuit is that Amplified Nation posted a layout of a real Two-Rock JM Sig that he had in his possession and around that same time, Ceriatone offered a layout of their Joyful Music amplifiers which is supposed to be very close to the Two-Rock. When I built my JM Sig circuit, I used a Ceriatone kit so I went with their layout 1:1 for the first round. The amp sounded great with Celestion G12-65H speakers and was very Fender-y to my ears. I added a switch to my amp that would toggle between the adding the bass jumper and removing it. Sure enough, adding the bass jumper changed the tone knob interaction quite a bit and lining up settings to pictures of John Mayer's live performances seemed to nail "that sound" of his!
Below is a gallery for full screen viewing
Ceriatone-Style with no bass pot jumper (According to this layout) Joyful Music tone stack on the bottom of the AC analysis.
I've added a YouTube video going over how I'm using LTSPICE and walk through how I'm manipulating the circuit and viewing results.