Yeah, those pinouts should work pretty well. You would of course want to get the CLK/!CLK into the pairs-version somehow. Or in another cable I suppose, if that's not so irritating.
Diff pairs being used unbalanced (one side grounded) isn't ideal, but the crosstalk should be okay as long as the bandwidth is kept below ~100MHz (being the 1/4 wave resonance of the 1m cable).
Filtering doesn't need to be fancy, and can be done in many ways. It can be done digitally for example, though it's not ideal because you've got 100% quantization noise added -- a digital input pin is essentially a comparator, a 1-bit ADC. Debouncing and properly phased clocking (sampling) are ways to implement this.
Transmitters, definitely should be impedance controlled in some manner; typically, CMOS output pins are a little too strong for ribbon or multiconductor cable, so a small series resistance should be added (source termination), typically 33 to 100 ohms. Alternately, a bus driver can be used (the driver is even stronger, but also made to handle continuous heavy loads, not just intermittent switching loads), and termination placed at the destination end (typically a resistor divider with a Thevenin resistance matching the line). Of course, the latter consumes a lot more power, which is annoying.
Analog transmitters should also be terminated, to avoid oscillation. The cable is going to be <100pF, which shouldn't be a problem for many sources. Just in case, you can add some resistance (100 ohms should be good enough) to help dampen it.
That addresses basic signal quality, giving high bandwidth without peaking. To actually reduce bandwidth, we can increase the source resistance further, or modify it with reactances.
Ferrite beads are an easy one. Pick one with an impedance (usually as measured at 100MHz) a few times the line impedance. This isn't bad to begin with (it'll "take the edge off" better than a larger series-termination resistor will). If we pair it with a shunt capacitor to make a not-quite LC lowpass, we can take off even more.
Ferrite beads have a diffusion characteristic, i.e., in the absorption band, Z ~ sqrt(freq) (and Arg(Z) ~ 45 degrees, i.e., equal parts R and X_L). Working it out with a capacitor, we have a cutoff frequency around:
Fc = (Z_FB * C / sqrt(F_FB))^(-2/3)
Example: for a ferrite bead of 330 ohms at 100MHz (Z_FB and F_FB) and C = 470pF, Fc = 16MHz and Zc = 21Ω. That's kind of a low Z, but with the driver impedance in series with it, or if we want to add more resistance, it'll roll off quite gently and not overshoot. For this I think the minimum would be 100pF and somewhere between that and 470pF should give good filtering without screwing up signal levels too much.
ESD diodes are nice as well, maybe not strictly required with a shielded cable (and with female pins in the jack, less likely to be zapped by stray fingers) but nice to have.
For so many signals, you'll want to use arrays. Quads seem to be the most economical. Everything is available: resistors, capacitors, ferrite beads and ESD diodes, in chip form.
That'll serve nicely for the bit streams; the digital signals can be similar, or larger resistors and capacitors (1k, 1nF?). Probably wouldn't bother with LC filtering. (RC filters are also quite soft rolloff, and combined with the increased risetime, some digital filtering may still be desirable.)
Analog signals can be active filtered if you like, but that's probably not necessary. Maybe reserve some space to patch in better filters, in the extreme case that it's necessary? Idunno.
Tim