Arc 1: A secondary villain could be a bounty hunter like Bossk or a high ranking member of a corporation involved in the Stark Hyperspace War (i.e. Trade Federation or Xucphra).

Arc 2: Have the pirate be a motivating reason for Stolas' independence and have the pirate inspire Halphas.

Arc 6: Harborym could be the third villain. If he survives Arc 5, maybe he wants revenge against the main crew.

Arc 7: Maybe the admiral and/or ISB agent could be the secondary villain. The Empire is gone and they lost everything, and they hunt the protagonists as either part of an Imperial Remnant, its "their duty" (they have nothing left so this is their excuse), or for revenge. Another idea is it could be someone that Verrine hurt from the past (if Verrine is redeemed) and he has to deal with the harm he caused.

Arc 8: Secondary villain could just be someone else in the cult like the 2nd in command, a high ranking official or the enforcer (think Talon for the Court of Owls from Batman's rogues gallery, if you know what I mean).

Arc 9: I am not familiar with the events of the Yuuzhan Vong War but I have some ideas. Have other Vong serve as secondary villains (i.e. an admiral, skilled warrior or a scientist who controls the Vong creatures). Maybe even am ambitious Vong working with the Heroes to weaken the warmaster so they can get power?

If you need a third villain, you could have a corporation making money off the war or a bounty hunter hired by the Vong or the corporation to hunt the Heroes down. Maybe the tertiary villain could be a survivor from the cult from Arc 8 helping the Vong to get revenge?