For choosing the filter part values, determine how much attenuation you require and how far away it needs to be. Open a textbook on filter design, and pick an architecture that will meet your needs in as few sections as possible. The book should give you filter prototype tables with values, which you scale up to your frequency and impedance (the filter prototypes are generally given at Z0 = 1 ohm and FC = 1 rad/sec).
Look at the bulk current injection test setup to determine the impedance of the signal injection circuit. That will be the impedance you'll be working against for designing the filter.
Since you have PWM/clock signals with sharp edges, you should aim to pass the 9th harmonic (or higher, if reasonable) with little amplitude or phase distortion. Square waves contain purely odd harmonics (3rd, 5th, 7th, etc) according to their Fourier series expansion, so you need to retain several harmonics above the fundamental frequency to keep the signals' corners sharp.