Do you have a specific definition of the confinement factor which you would like to use? If so, I may be able to help you with that.
We do have a modal volume analysis group in FDTD Solutions which can be used to characterize the size of the resonant mode, and there’s more information about it here:
You can also analyze the Q factor of the cavity to characterize the resonant frequency and decay rate of the resonant mode supported by your structure:
Regarding determining the wavelengths at which power flows into the substrate, I would suggest adding a 2D frequency domain power monitor at the interface of the cavity and substrate and looking at the transmission result through the monitor which will give the net power flowing through the monitor into the substrate as a function of wavelength or frequency. By default, the transmission result is normalized to the analytic power injected by the source, so if you are using dipole sources, you may need to re-normalize the results by the power which is actually injected by the dipoles which is discussed here:
I hope this helps!