Class variant/ Prestige Class

[Rev Haus 235]

I'm trying to make a class variant or prestige class for the campaign that i'm playing in. We play in Iron Kingdoms, and the goal is to make a rogue variant who is dedicated to one of the gods of the realm.
Basically the class is an appropriator of goods for the temple, using his rogue abilities to acquire items at all cost.

It's basically just a rogue class with one special ability added to a normal rogue class. The class is supposed to be an over lay, so that the class counts as normal rogue levels. At the first level it allows the user to build a focus device which is basically a magic item. Then once a day per two levels, the character can use the ability of the magic item.

My problem is, I can't figure out how to make this happen. I can copy and make a variant class, but I'm not so sure how to make the special ability work. It's also treating the variant class like its not a rogue class, which it should be. This is causing issues with the level related class abilities for the rogue class.
Any help with this would be awesome. Thanks in advance.