Give this a try and let us know how it turns out. Bass and Treble control added and original Tone control removed. I also omitted the presence trimmer.
The Timmy bass pot is a high pass filter which started cutting frequencies between 48hz and 1.23khz depending on the pot position. The Crunch Box used a 1K resistor and 220n cap for its high pass filter in the same position which starts cutting bass frequencies from 723hz and down. I've altered the caps in this bass control to 100n and 3.3uF which will alter the corner frequency of the high pass filter from 48hz to around 1.5khz and so close to the same range as the Timmy. If you alter the 100n cap to a 120n then it will be exactly the same. This range means when the Bass pot is approximately half way, you will be getting the same response as the original Crunch Box which should make it ideal, allowing you to tweak both ways.
I'm not sure how useful this entire range will be with the Crunch Box because it was done to allow you a bit more of a bass boost with the Timmy when using it with cleaner settings. With the Crunch Box in high gain mode it will start to get a bit flubby in the low end, but at least you have the control to pull it back a bit as you need to.
The Treble control low pass filter, will cut high end around the same frequency range as in the Timmy (there is an additional 470R of resistance in series with the pot, but that won't change it too much).
The Timmy had the final opamp stage after the Treble pot whereas this goes straight to the volume pot, but that should be fine because it's how the original Crunch Box did it anyway, just with a different frequency range.
Anyway give it a go and let us know what you think. If it's a good mod I'll add the layout to the main site.