I would run this AD skill system with "Spacer Skills Revisted" SFman 10. PCs start 2nd level spacer skill for their position and prerequisite skills specified by "Spacer Skills Revisited". This will mean that the pilot character is able to pilot an interstellar craft of HS3. 

Multiple missions much like WoWL module- 

Alpha: undercover mission to Dark World station. Document ships present, compare with files assembled by Streel, attempt to find out where and when suspected pirates are headed out. Track them to their hunting ground and when they engage in piracy take them out. If they should encounter a known pirate just take them out but avoid revealing their true mission. If they uncover any evidence of the fabled location of "Tortuga" the pirate planet they are to report its location at once. 

PCs will need a cover. And Streel will likely arrange for a fake piracy hit on a surplus tramp freighter. 

There will be an inner Reach militia contact. They can deposited pirate prisoners with the Inner Reach militia which can disappear them at a black site equivalent to Guantanamo Bay (Space Fleet cannot do that due to laws and regulations). Perhaps a Star Law contact? 

Alpha mission involving undercover work on Dark World leading to going after a suspected pirate. 

Beta mission: known pirate spotted at Dark World , PCs must develop intell to be able to run them down or report their destination to Inner Reach militia or Space Fleet. 

Gamma mission: finding the fence, pirates must fence their cargoes and csptured ships somewhere. 

Delta mission: Fables of a Pirate Planet