First.. Ranked Talents? Can you keep purchasing the same talent for ranks in that talent? For example Toughened for a cost of 5.. Can you keep purchasing that talent to increase its rank?

Second: Stim Application(Supreme), Is this a permanent increase in a Characteristic? Or temporary?

First question is a NO. However you can purchase more of that talent deeper in the tree, as with ranked talents there are usually more than one in a spec tree.

Duration is explained in the base StimApp talent, it's for an encounter.

You can't repurchase a ranked talent in the same slot on the same tree. To increase ranks you have to buy the talent again at a different location on the tree, or in another tree.

Stim application, of all types, bonus only lasts utill the end of the encounter. It is not permanent.