So basically the FC will have to step up its intelligence efforts, hand over information to local police (made up of local Pashtuns) and empower the Majority of the people of KPK and Baluchistan to be able to limit the ability of these miscreants to operate and regenerate. A slow process, it doing everything legitimately, through the courts is the only way to maintain trust in the rule of law.
This is why rule of law and a fully documented economy as IK proposes is so important. Dry up any resources for the miscreants operating outside the law and reward those living normally in both KPK and Baluchistan, by spending tax money raised in there areas on better services for the people of those areas. More services into even the most remotest of areas will make people feel a better connection with the rest of the nation, and a stronger sense of belonging. Hence, why IK wants to build Namal university. Bringing back IK, will remove nearly all of wind out of sails of these miscreants.
Not rocket science, just better governance and management, while denying the miscreants from operating in any significant manner, especially through the use of local police forces, made up of preferably people from literally that exact area (except for people with personal vendettas with the miscreants, as not to make it a personal matter).
As for the border, I hope the army gets long range sound or microwave systems to attempt frighten away the miscreants. With all encounters filmed (with facial recognition software, to be used to deny a visa or find a way to arrest later on if necessary), a clear demonstration of escalation only when repeatedly provoked by the would be attackers, so that if the need arises to switch to lethal force, in the court of local public opinion, it will be perceived as justified.