I assume you are referring to this schematic at
http://www.dancook.name/cougar_contr...r_power_2d.pdf
The schematic on the wiki shows the capacitors are placed in parallel with the power supply (between V+ and GND). I also tried this configuration but it had no noticeable effect on the output waveform.
The schematic on the wiki does show the "flyback diode" in parallel with the inductive load (motor). I tested this configuration and showed the O-scope output above.
I tested capacitor and diode in parallel with the load (from Drain to V+). See the attached circuit. The resistor I used was in series with the capacitor only, not in series with the motor. You are correct that a resistor in series with the motor would be a very bad idea.