The input cap is already plenty big enough for bass. That's not where the low frequencies are getting lost. The easiest way to make a RAT better for bass is to do the Ruetz mod, but it sounds like you've already done that and still need more low end. The Ruetz mod sets the LF roll-off to around 60Hz and we can do even better. You could double the size of the 4.7uF capacitor to around 10uF (the one series with the 560ohm resitor). This would move the roll-off down to 28Hz, which would let most of your low end through.
That being said, I find that the main problem with distortion pedals is not that they don't let enough bass through. Rather, the problem lies in the fact that they generate a lot of high frequency harmonics that drown out the low frequencies. The best solution in that case is to add a clean blend circuit, or use a clean blend pedal. If you just want a bass boost, you could add a simple lowpass RC filter to the clean blend signal so that you would just let through the low frequencies in the blended signal, but I usually find it's not necessary.
The final option would be to add a bass boost circuit to the output stage instead of a clean blend, but that's a lot more complicated and requires a good deal of circuit design knowledge to implement well.
Last edited by Projectile : 01-24-2013 at 08:41 AM.