The EMG pickup 'sees' its own internal preamp (just a single op-amp configured as a differential amplifier) and the tone/volume controls are buffered from the pickup inductance and self-capacitance. The resonant frequency isn't therefore affected in the same way as a passive pickup by tone control loading or cable capacitance, so isn't useful in calculating tone control values.
The way I would approach this is to use a couple of short clip-leads and try different caps until I got the one I liked best. You could model the tone stack and output impedance of the amp (10k ohm) in PSpice and do an AC sweep analysis to visualise what's happening, but in the end it comes down to your hearing and perception of the sound. I've found that changes to EMG caps need to be fairly drastic to make meaningful/useful differences to tone.