Not to point out something very pertinent in your analysis or anything. But do consider the fact that India was able to not only survive but put down the only viable secession movement in India - in Kashmir, when India was at her nadir and Pakistan in terms of power(economic/military/diplomatic) was at her zenith vis-a-vis India.
Today, i feel you donot realize just how much the circumstances have changed. How much India's military, economic, political/ public relations strength has grown. And India has left Pakistan miles behind in this great game. India is not as straitjacketed as it used to be in the 90's. This is the macro scenario in which you believe Pakistan can achieve success of a secession movement in India by its backing.
When it comes to micro scenario - India has used the past decade to completely ramp up its infrastructure related to Pakistani pushing of insurgents across borders. From deploying more troops to having better equipped troops to employing a whole host of technologies and obstacles to make infiltration multiple times tougher than it used to be in the 90's even if Pakistani Army fully backs such infiltration bids.
Regarding funding/backing other movements using BD or Nepal. Well, BD has changed too.
Today India can spread secessionism in Pakistan without a corresponding and an equal counteraction even with US remaining neutral to both sides by sheer gains that India has made. And in any such venture of both India and Pakistan, today India does have the wherewithal to be more effective.