How can I generate an output of simulated truth data, rather than reconstructed

If running on one file i.e. as in your Run_XXX.C script, you may just change the HipoData type to HipoTruth. Then any output variable calculated in Kinematics will be calculated using the truth 4 vectors passed from the Lund file. e.g.

HipoTruth hdata;
hdata.SetFile("/my/simulated/file.hipo");