Two-plane-wave source simulation is doable, with some strategy.
since they have different spectrum, and the result is normalized to the source (Understanding frequency domain CW normalization), I would suggest that you do two separate simulations, and sum the result coherently. For angled incidence you can use BFAST and if the angle is large, say 70 deg or above you will need to use Bloch BCs in the plane of tilt to sweep wavelength.
Lumerical FDTD always uses a pulse for the cause of simulation efficiency, except for rare cases where a CW signal is required.
Polarization is what you want to simulate. It is up to you to choose. Usually s and p polarization may have different responses.
Once you get sum of the coherent result, using gratingpolar script to get the amplitude quantities: https://optics.ansys.com/hc/en-us/articles/360034407034-gratingpolar-Script-command
you can get the summed power transmission/reflection for each order. Please make sure that you added them from the same diffraction order, which is in the farfield.
If you want the fields inside the grating, you can use script to get the E fields from a monitor covering the region you desire.
Band structure simulation is relatively easy. Please refer to the photonic crystal examples: https://optics.ansys.com/hc/en-us/sections/360006919074-Photonic-crystals
As long as you know how to quantify the coupling efficiency with a formula, eg, transmission=transmitted_power/source_power, you will be able to extract it from simulation.
Since your questions are quite comprehensive, I would suggest that you do it one by one, and write new post for each question so to isolate posisble issues. Otherwise it might lead to some confusions. Please try the easy one first.