I'd try around 70-80Hz, you could get that just by adding another .001uF in parallel. You may even need to go lower and use a third .001uF cap for about 50Hz, but I doubt it.
edit: btw, .001uF and 1Mohm is 159Hz. And how is 4th string 2nd fret an E? Isn't that an F? Or do you mean on guitar? In that case it'd be 330Hz at that fret, 165Hz at the 6th string open E. Lowest note on a bass is 82.5Hz, but the Q of a filter like this is probably pretty big so I think 80Hz or possibly even lower would work.
edit 2: Wait, by the diagram it looks like you have it wired as a volume knob with a treble pass, not a tone knob.
Volume:
It should be wired like this, in parallel with the output, not in series: