The cross-ID's between index and mass are at the bottom of the input file which comes as part of the source code package. The example here refers to a large mass grid or isochrone on large grid. For a small mass grid, you would have chosen 5,5. This does not appy to the full isochrone model since the mass grid is variable. This parameter controls the time step to print out the spectrum.
Detailed explanations are in the sp-feature subroutine.
These are options to generate various outputs. We recommend to select all files, unless you are very familiar with the code. Some of the subroutines are interrelated. If you choose such a subroutine but not the other, required one, a warning will be issued. The 14 output flags are explained below.