For your PWM signals, the 50kHz PWM frequency matters less than rise time.
The bandwidth of your square/rectangle signals is directly related to the rise time. The faster the rise time, the wider the bandwidth. Many modern MCUs have output rise times in the nanoseconds, which means bandwidth up to hundreds of MHz. A great opportunity to turn any cable into a wideband transmitting antenna!
While digital signal bandwidth comes from rise time, frequency also matters. Each edge acts as a pulse of RF that can be radiated by the cable, but frequency determines how often that happens, so a higher frequency digital signal will want to radiate more energy simply because it has more edges.
In other words, if you add a simple resistor in series at the source, like 33-75R, it will slow the edges a little bit, reduce bandwidth, and add some impedance matching. This will avoid many headaches, even if the impedance matching isn't perfect... and you won't need to worry about a ground plane in your cable.
Since the goal is to limit signal rise time, and current pulses charging and discharging the transmission line capacitance, the resistor should be on the driver side, close to the source of the signal.
Signal layout for your FFC is the same as for ribbon cable, from highest to lowest signal integrity:
One GND between each signal ; order the signals to keep some distance between potential crosstalk victims and aggressors
2 signals, GND, 2 signals, GND... this ensures each signal has at least one GND next to it
Add decoupling caps between supply and ground at both ends of the cable, to link VCC and GND at high frequency. Now, VCC wires in the cable can play the same reference role as GND with regards to signal integrity. This is useful if you need several VCC wires in parallel for the supply current you need, or if you have several supply voltages, they can act as "free" reference wires (still costs the capacitors though).
Then you can cluster your signals, have one side of the cable with crosstalk aggressors, highspeed but insensitive signals, and several reference wires in the bunch, then on the other side of the cable more quiet signals that won't need as many reference wires.
For lower cost (and lower integrity), keep deleting reference wires until a problem occurs.