Looks near perfect Matt.
The only issue now is to either remove Large Missile and Torpedo Bays. You're not going to lose anything as 5-medium torp/missile bays are identical to the large one... but you do gain the much needed clarity about the +4 to-hit and +1 damage per die applying only to direct fire weapons. (It doesn't make sense to apply those bonuses to missile/torp weapons).
The only issue now is to either remove Large Missile and Torpedo Bays. You're not going to lose anything as 5-medium torp/missile bays are identical to the large one... but you do gain the much needed clarity about the +4 to-hit and +1 damage per die applying only to direct fire weapons. (It doesn't make sense to apply those bonuses to missile/torp weapons).
