So, I think I solved my problem by using the DBUS interface into the Ekos Align module to set the Target Coords. Roughly:
... bus = dbus.SessionBus() align_object = bus.get_object("org.kde.kstars", # Connection name "/KStars/Ekos/Align" # Object's path ) ... # after slewing ... align_iface.setTargetCoords(target_RA_value, target_DEC_value)