I ,too, tried everything to make my RAT sound good: first the ruetz mod,then Vodka mod (really serious one that involves replacing the chip and some caps).After all that I was still dissatisfied with the sound I was getting with it - it was harsh even at the low settings.Plus it cuts a great deal of bass frequencies.I spend hours tweaking it and still couldn't make it sound good.So I just put it aside and bought Xotic bb-preamp instead. Now I'm much happier with my tone.
I think it is the RAT Kurt uses in Brooklyn Sometimes.He sets it very low sort of like a booster more than distirtion.
I know Kurt using used Xotic AC-booster for a while but then came back to RAT again.I assume though that he uses it with X-blender which allows the natural sound of the guitar to come through (RAT is not true bypass). Maybe that's is the secret...