The trick with this is to kill the low end gain in all the gain stages, remove some high end in the 2nd and/or 3rd stage (usually just the third with the SLO based amps) and get back your low end by achieving high amounts of attenuation in the tonestack. What the attenuation does is provide an apparent "boost" to the highs and lows. Generally in high gain amps, if you want more bass you can increase the value of the bass pot. Further bass boost is achieved through more attenuation in the power amp section's Global feedback circuit in Phase Inverter driven power amps.
To Jon, the Lee Jackson you posted is probably not the best amp for a beginner to learn to mod on, it strays way too much from the basic, classic and historical design. I would say you are better off building something like the gain stage of an SLO or something similar and modding things to taste. With that you could even throw a clean channel in there as you would have half a tube not being used. A switch or foot switch jack, a relay and a connection to a low voltage would be all you would need for basic channel switching.
Also Jon, the reason that you are not getting huge results with decreasing the cathode bypass caps is because you said it, you increased the gain on the stages by decreasing the cathode resistor. This mitigates the effect of the bypass capacitors. Its a long explanation with some equations, I am more than happy to explain, but simply put, when a cathode bypass cap is being used, the gain of all signals above the resonant frequency will be as if there was no cathode resistor in terms of gain. All you are doing when you mess with the gain via the cathode resistor is increasing the gain on the low end, the gain on the highs never changes. Try going back to the stock cathode resistor values, and decrease the bypass caps on V1a (C1) and V2a (C3) to 1uF.