Fix bug when applying TDCF and sampling the line uncertainty

This MR fixes a bug where using both TDCF application to data and sampling the line uncertainty resulted in values calculated for kappa_c and f_cc were incorrect. This is because the calculation of "this_S" did not include the mean measured optical gain.

This also resolves a potential issue that the Pcal correction factor having an unintended extra delay.

This MR also sets a default value in case no line uncertainty threshold is given