It turns out that after the previous changes made in this file, the issue where the Q's Men ships fire at the player after the race still occurs. Unfortunately I wasn't able to fix this, even after 5 hours of trying because the FL mission scripting engine doesn't really seem to agree (one of the two ships just always kept firing at the player, despite it being friendly to the player, no matter what). Instead, I've made the ships fly away at cruise speed to a different location. This way they just mind their own business and don't attack the player.