Hi mwolter,
What sort of accuracy do you require the pulse width (duty-cycle) measurement? This essentially determines the timer's speed. The examples earlier in this thread are designed to read a radio controlled receiver, accurate to 1 microsecond, would that be enough for your project?
It might also be possible to use timer TCC2, if you're not using it already?
Also, which pin would you like to receive the incoming signal, any pin can be used except the Non-Maskable Interrupt (NMI), which is digital pin 2 on the Arduino Zero and digital pin 4 on the M0 Pro/M0.
The pulseIn() function blocks while waiting for the pulse, thereby making it unsuitable for time critical projects.