So as I understand it Primed Thrusters allows for a boost or barrel roll even with 2 stress tokens. But PTL states after you perform an action you may perform one free action. Does this check the stress and not allow or does primed thrusters overrule this as well.

In words for clarification:

Silencer pilot has adv sensors, ptl, and primed thrusters. Start of activation has 1 stress token. Before reveal adv sensors for boost, push for focus, this push gives a second stress token. Can you do that push? Or can you push but only for a BR because you would have had 1 stress token before, preventing the focus action?

You could only push the limit into other Boost/Barrel Roll actions. Like other actions, normally free actions cannot be taken while stressed, so you couldn't focus. Primed Thrusters carves out an exemption for Boost/BR only, and only if you don't have "too much" stress.