You can do the differentiation in space domain or wavenumber (k) weighting in spectral domain. Basically:

space domain: slope s= dh/dx

spectral domain: S_slope(k)=k^2 S_elevation(k)

S_slope is slope spectrum, S_elevation is elevation spectrum, h is elevation,d x is sample spacing, wavenumber k is related to wavelength L by k=2pi/L.

The spectral approach gives you statistical comparison, and is probably much more preferred for your case of comparing lidar and WaMoS measurements (or for data sets from different sensing systems in general.)