Alright, so again, a fairly straight forward question.

Are there any hard and fast rules for improving the quality of armor once it's acquired, and improving it's systems? Or would you need to use the "Trade-In" rules of Black Crusade and essentially just acquire a better set of armor with all quality and systems built in? Thanks!

You can find Armour Upgrades in Hostile Acquisitions . You can add those after the Armor is created (although for some Upgrades, like Lathe-made, it doesn't make sense you can add the property to an existint armour).

For Armor Craftsmanship, I think you have yo buy a new Armour, you can't Upgrade Craftsmanship (at least, no by RAW).

There are crafting rules in Dark Heresy's "The Inquisitor's Handbook" which include upgrading armour by one step of quality.