I keep the Master Volume around 8 as well, and then run my lead volume above 3 (louder for gigs). I know exactly what you're saying about the input gain - if you run it too low, the tone falls apart and sounds pretty terrible.
Essentially, if you open up your amp you'll see a capacitor across the input gain potentiometer. What this does is keeps treble in the signal as you turn down the pot - it has no effect the further you turn it up! This is why you get less treble as you turn the gain up. So what you can do is experiment with no capacitor at all, or different values. My doing this, you'll get a meatier sound even with the gain turned lower since not as many treble frequencies are passing through. The real explanation is that as you increase the value of the capacitor, you allow more frequencies through. Jubilees use 1000pF capacitors which allows quite a bit of frequency through - by reducing this value, you are kind of "snipping" the upper frequencies and therefore getting a less middy/trebly sound. Experimenting is key here: I've found that with no value it's a very flat sound, but with 1000pF it's a little too fizzy for me. I'm in the process of trying out 500pF which would be right in the middle.
The LED mod is simple as well. Basically, you'll see two red LED's inside the amp acting to give more overdrive. It's basically like having a Tubescreamer built right into the amp to push it more...believe it or not, all that tone and goodness in our Jubilee's are from tubes mixed with LEDs! So you can use different value/color LED's here to cater to what you want to hear a little bit. Carol Ann posted here a while ago saying that he prefers using a combination of a 5mm green LED and a 5mm red LED for a more "classic rock" sound and not as much of an "80's metal sound". I haven't tried this mod yet, but when I get home in a few weeks I'm going to try it.
The cool part about this mods is they are easily reversible...and you can put them on an spdt toggle switch so that you can switch between the original circuit or your new "modified" circuit if you want.
If you try any of these mods, don't blame me if something goes wrong! They are very simple mods, but make sure you know what you're doing or take it to somebody that does I've had a few years soldering and modifying amps and pedals so I feel pretty comfortable.
"The way I like to look at it is....if that's the last time I ever got to play, I'd better give it everything I've got." -SRV